Thank you to all who have posted such helpful information on this forum. My brother and I will be in CR from May 8-16, and would like some advice finalizing our itinerary.

Day 1. Sleep at SiempreVerde B&B
Day 2. Doka Coffee Plantation, Poas, La Paz, sleep at Arenal Paraiso
Day 3. Arenal National Park, hot springs?
Day 4. Day trip to Cano Negro
Days 5-8. We can't decide between flying to Osa (staying at Bosque del Cabo) and ending the trip with Los Angeles Cloud Forest or driving to Monteverde and ending with Manuel Antonio.
Day 9. Early flight back home

Since we'll be going at the start of the rainy season, I'm apprehensive of the weather at Osa. However, I've read that Monteverde can be crowded and MA is unimpressive compared with Osa. Any thoughts or suggestions would be greatly appreciated. Thank you!

Los Angeles Cloud forest is actually near La Fortuna/Arenal. You would just be back tracking to go there after Bosque del Cabo.
As far as worrying about the rain,there is a good chance you will have it in Monteverde also.
You will only have 3 days so I would choose one place to go after Arenal. Manuel Antonio has the most to offer and would be the closest to get back to san Jose.
Day 1 Alajuela
Day 2 La Paz, Doka, night at Arenal Paraiso
Day 3 hiking, hot springs
Day 4 Cano Negro
Day 5 Transfer to Manuel Antonio (5-6hrs) night in MA.
Day 6 Manuel Antonio tour
Day 7 Mangrove tour (highly recommended)night in MA
Day 8 Highly recommend you head back to San Jose today if you have an early flight the next morning. It takes 3hrs to drive to San Jose from MA and you need to be at the airport 1 1/2-2hrs before your flight. Don't forget to pay the exit tax ($26) before getting in line to check in.
Day 9 leave the country.

ok, we've revised the second half of our trip:
Day 5: drive to Manuel Antonio, stopping at LACF along the way, stay at Costa Verde
Day 6: Canopy Safari tour
Day 7: kayaking mangrove tour
Day 8: hike in MA, drive back to Alajuela, stay at ?
Day 9: leave Costa Rica

Some questions: will we have enough time to stop at LACF on the way to MA if we leave at 7am? What's a good car rental place in San Jose (checked Dollar but it seemed they only had manual available)? Is there a cheap hotel close to the airport that still has some character?

Any other suggestions? Thanks once again, from one Suzie to another!

You might want to check Adobe Rental car...but don't know why manual is a problem for you?
As for inexpensive hotel in Alajuela, check out Orquideas Inn. Great place. I've stayed there several times.

Regarding LACF....it is only about 12 miles from San Ramon where you will be going through to get to Manuel Antonio. I have not actually been on those 12 miles so can't tell you how long that trip could be. 12 miles can be a very long ride on bad roads. There have been a few people on this board who have gone there fairly recently. I hope they see this and can give you more complete answers. I don't see why you wouldn't have time for a quick peek if you do leave very early. My only issue is you leaving your things in the car. It is never really advisable because of theft. Some places do have pretty secure parking but other places like Carara are well known for theft of personal items from cars. Most of the problems are around the more visited areas which the LACF is not. You might want to contact one of the lodges in that area to see if you could park there for an hour or so.
If you do stop in the cloud forest watch the time. The road is a pretty straight shot once you pass Jaco and even a little before. If you do find yourself driving in the dark for the last little bit don't panic. You will find your way just fine. By this time you will be pretty sick of those african date palms.
For car rentals, a lot of people on this board have had good luck with Adobe.
Don't know if you have seen my other postings but try to have the car delivered to your hotel in Alajuela rather than picking it up at the airport. It might save you a huge airport tax.

A couple of places to stay in the Alajuela area possibly would be Orquideas Inn or Vida Tropical.

We used Elegante for car rental and all was fine.