I'd skip staying in Santa Cruz and go directly to Monterey or Carmel so you've got a full day in the area. Otherwise, better.

My vote is to ditch Yosemite altogether from this trip, and stick to what you were really interested in - the coast. And with just 6 nights, really you have 5 days plus 2 travel days.

Fly into San Francisco for a couple of nights, then take a coastal drive down to Monterey (see Gardyloo's itinerary). If you really want, you could drive down farther, but I wouldn't want to try for all the way to LA. Not with your timeline.

If we do go for Yosemite, where would you recommend we stay the night?

IF you include Yosemite (and that will be REALLY stretching yourselves thin) the only places to stay are in Valley (most likely at Yosemite Valley Lodge -- known to most of us a Yosemite Lodge at the Falls). If they are fully booked, the Yosemite View Lodge in El Portal is the next closest accommodations.

Anyplace else - even though they advertise as being 'close' to Yosemite - will be 90 minutes or more drive from Yosemite Valley.

Five nights really doesn't give you 6 days -- and a lot of the time you have will be spent in the car.

"If we do go for Yosemite, where would you recommend we stay the night?"

As you've seen, many opinions on whether you should keep or eject Yosemite! If you decide to keep Yosemite and fly out of Fresno per your latest itin, I'd suggest the following:

Within Yosemite - as you will quickly see, there are only 3 actual hotels/lodges technically within the park (unless you are interested in tent cabins/camping). In mid October, you should have a decent chance to reserve and/or pick up on a cancellation at one of these 3 that include: 1) The Majestic - think grand old historic hotel - 5 star back in it's glory days but now more of a fading relic. The common areas are still amazing and I've enjoyed my stays here but you have to go in with the right (low) expectations on the actual rooms and realize you are paying a high price for staying in an historical lodge in a prime location.
2) Yosemite Valley Lodge - similar to the Majestic, you are paying for primo location. In this case, for a 1950's style motel. Sometimes we stayed here when we wanted to "splurge" from staying in the Curry village tent cabins... Awesome location.
3) Big Trees Lodge - this is a ways down the road at Wawona so not in the middle like the first two. I've only stayed here once and it's far enough from the valley floor that IMO you might as well consider staying in Fish Camp or other places on the borders of the park.

Outside Yosemite border - since you might fly out of Fresno, I'd suggest you look at one of the options in Fish Camp as it would be on the way to Fresno- there are some well rated B&Bs, etc.

Back to your revised itin - are you now planning 7 or 8 nights? It will take you about 1/2 day to get from the coast to Yosemite so you really need 2 nights in Yosemite IMO so you can at least have 1 full day to do a hike/spend time in the valley. I will not try to dissuade you from Yosemite as it is one of my favorite places in CA and I spent a lot of time there in all seasons when I lived in the Bay Area. With that said, you are signing on for more driving to make the side trip there so it really comes down to whether see the grandeur of Yosemite vs more time on the coast is worth it. It is true that by October, Yosemite falls may/will likely be a trickle vs the roar you get in the spring but the valley and rock formations are gorgeous at all times.

So, if you keep Yosemite, you may have to steal some time from the coast. I suppose you could get up super early on day 7 and drive to Yosemite to enjoy 1/2 day and then spend 1 night and get up early the next day to do another 1/2 day IF you are able to get a later flight out of Fresno (but assuming you are from eastern side of US, that may not be possible as Fresno airport is pretty small and assuming you are connecting).

Santa Cruz/Monterey/Carmel/Big Sur all have their own character but again, you'll need to trim time if you keep Yosemite. Santa Cruz has the beach boardwalk and feels a bit more quirky and economically diverse but you get the same or better coastline views further south. Monterey has the aquarium. Carmel is upper scale "quirky" with lots of boutiques and more expensive restaurants, etc. Big Sur is all about the coastline views. So, I agree with MmePerdu that you might cut Santa Cruz and stay 1 hour further south in the Monterey/Carmel area as a base so you can explore the coast between there and Big Sur before heading inland. You'll still get to have the drive from SF past Santa Cruz on the way to Carmel area and unless you are really into seeing the boardwalk (great for my 6 year old but otherwise I could easily do without), you will have a great sampler of SF/Coast/Yosemite with your plan!

>>2) Yosemite Valley Lodge - similar to the Majestic, you are paying for primo location. In this case, for a 1950's style motel.<<

All of the rooms have been updated, still fairly rustic but not 50's-ish.

>>I'd suggest you look at one of the options in Fish Camp<<

Yes -- Fish Camp is good for Fresno -- but not so much for the Valley. It is nearly 1.5 hour drive from Yosemite Village.

Looking at your 1:05pm plan, I would visit Santa Cruz but move on to Monterey for that night and have 2 nights there.

And if you decide to skip Yosemite, take the Big Sur drive down to Cambria on day 6, visit Paso Robles or just the Cambria/Morro Bay/San Luis Obispo area on day 7 and fly home from San Luis Obispo.

On your 2nd afternoon in SF, you could drive to Muir Woods. (If you do plan to explore a bit from SF, you might want a hotel such as Columbus Motor Inn where parking is included.)

If you leave Yosemite out, I don't feel Debbie's take adds particularly to the quality of your trip. I'd rather see you spend 4 nights (3 full days) in San Francisco and the balance of your time (however long that is, I'm confused) using Monterey/Carmel as a base for the rest of your trip, including a day on the Big Sur coast.

>>On your 2nd afternoon in SF, you could drive to Muir Woods.<<

I wouldn't -- Henry Cowell and/or Big Basin are better parks w/ MUCH smaller crowds and either would fit in w/ Santa Cruz and south.

This is all so helpful- thanks everyone! To be clear, we are staying 8 days, 7 nights. We are also pretty happy to fit a bunch of stuff in during that time- we like fast-paced vacations. We will also get in to San Fran by mid day and will shoot to fly out of either Fresno or San Fran as late as possible to make the most of our time (haven't booked flights yet so not sure what exactly will be available). We feel very strongly about fitting in Yosemite, so we've made a few tweaks to our plan as of right now, including skipping the night in Santa Cruz as many have suggested:

Day 1: Fly in to San Fran. Explore the city.
Day 2: San Fran
Day 3: San Fran
Day 4: Wake up early and start the drive to Monterey (@3hrs), stopping in Santa Cruz to visit Henry Cowell State Park. Arrive in Monterey and see the aquarium and the wharf. Do the 17 mile drive/ visit Carmel. Stay the night at Mission Ranch.
Day 5: Drive to Big Sur (@1 hr. drive) Perhaps a horseback riding tour? Drive back to stay at Mission Ranch again.
Day 6: Drive to Yosemite (@3 hr. drive) Stay at TBD.
Day 7: Yosemite- half dome village bike tour, tioga pass. Stay the night again at TBD
Day 8: Drive to Fresno and fly back to FL.

Thoughts?? :)

Doable

It will be rushed to squeeze in Henry Cowell and the Aquarium on the same day but doable-9sh. That will be a 3+ hour drive plus the stops. So say 2 hours at Henry Cowell and 2 hours at the Aquarium - it is a 7+ hour travel day.

Skip the 17 mile drive for sure -- do Point Lobos instead.

It will be much more than 1 hour driving into Big Sur, exploring and back -- count on at least 3 hours total (including lunch at Nepenthe)

>>Day 6: Drive to Yosemite (@3 hr. drive) Stay at TBD.<<

The TBD should be the Yosemite Valley Lodge (or the Ahwanee/Majestic if it fits in the budget). If you can't get in there -- Yosemite View Lodge in El Portal. Anyplace else will be a very long drive into the Valley and you don't have the time to waste.

Count on a 4.5 hour drive into Yosemite Valley.

Great- thanks. I'm not familiar with Point Lobos... how is it better than the 17 mile drive?

Also, what specific things should we do in Yosemite? We definitely want to do the half dome village bike tour but are there an other must-see places/activities? I'm having a hard time grouping the Yosemite days together based on locations around the park.

Lastly looping back to San Fran- we need to figure out which area to stay in. We're typically fans of staying in more local/residential areas in an air bnb but I'm thinking we might favor a more touristy location so that we're central? Any advice there would be great. And any advice on must-see things other than alcatraz and the golden gate bridge which are on the agenda. :)

17 mile drive is about golf courses and "fancy" suburban-ish houses. Point Lobos is about nature. Depends on your interests.

If it was me -- I would probably skip the bike tour. If you had 3 days -- sure, but you will only have 1.5 days. I'd go up to Glacier Point, and I'd maybe do the Mist Trail.

Point Lobos: "the greatest meeting of land and sea in the world"

http://saveourshores.org/wp-content/...is-Lincoln.jpg

http://www.hewlett.org/sites/default...%20Reserve.jpg

Big Sur is not a specific place (although there is a Big Sur Village with a few stores and restaurants, etc.). It is the 90 miles of coastline between Carmel and Cambria.
Also it takes more than one hour, you have to ignore Google Maps time estimates in this area, due to low speed limits and you will want to make lots of stops (Google assumes you make none).

Pt Lobos:
www.youtube.com/watch?v=DdVWNEHD-IM

McWay Falls:
www.youtube.com/watch?v=KuvCEtFrQwg

I wish you could stretch your trip to 10 days so you could see Yosemite and drive dow the coast to Cambria.

"Also, what specific things should we do in Yosemite? We definitely want to do the half dome village bike tour but are there an other must-see places/activities?"

With your short time in Yosemite, you'll have to make some tough decisions on what to prioritize but you'll love it no matter what. Probably the key question is whether you really enjoy hiking or would prefer to keep your hikes/walks more limited.

With limited time I would prioritize Glacier Point and the Valley over Tioga Pass and Southern Yosemite.

Also, as previously noted, ideally you are able to secure a room at either Majestic or Yosemite Valley Lodge so if nothing shows up, keep checking for cancellations! (BTW - to Janisj on my comment that YVL was "50's" style motel I was referring more to the outside access motel style, not the inside which was updated a bit but let's face it, not exactly modern....)

A few ideas you could bounce around given your mention of bikes and assuming you get an early start from Monterey and reach Yosemite Valley around lunch/early afternoon via CA-140.

Day 6 - Arrive Yosemite valley - rent bikes at Yosemite Valley Lodge or Half Dome Village (formerly Curry Village) and spend the afternoon exploring the Valley floor on bike. Flat and easy - you could stop and take a look at the Majestic (if you are not staying there), ride over to Mirror Lake trail, base of Yosemite Falls (likely a trickle in October), see the river, stop by the Royal Arches and see if any climbers to watch, etc. etc.

You could also combine your bike ride with a short hike as you can park your rentals at racks near trail heads - Mirror Lake, Columbia Rock, Vernal Falls, Lower Yosemite Falls, etc.

Day 7 – Take early shuttle to Glacier point (or if you are not staying in the park, you could drive). My favorite thing to do with friends who have not been to Yosemite before (BUT who enjoy hiking) is to take the Panorama trail from Glacier Point down to the valley floor. It is one of my favorite trails as the views are incredible and although it is 8.5 miles, it is net downhill and not that strenuous so long as you don’t have knee problems. Depending on how much we stop for photos, etc, it usually takes us 4-6 hours. After any hike where we end up in the Valley Floor, we must enjoy pizza and a cold beer at the Half Dome Village pizza deck :) 

If you want a shorter hike, there are several short hikes at the top of Glacier point. For hiking options, check out yosemitehikes.com or a similar site for some good descriptions of all your hiking options.

You could flip those two days of course if you wanted to hit Glacier point by car on Day 6 (assuming you don't do the Panorama trail)and then have Day 7 to explore the Valley floor and/or do a hike of your choice.

You can visit Point Lobos on Day 5 as part of your Big Sur day. The reserve will be open from 8am to 7pm in October. A good turn around point for the day is McWay Falls at Julia Pfeiffer Burns. There are horseback tours at Andrew Molera State Park but I haven't taken them. They ride along the hiking trails out to the beach and back.

For nature I'd recommend going north from SF rather than south. You can see a lot going south too, but going north there are more mountains and interesting landscapes to see.