I'm just days away from the start of my trip to Japan! I want to double check that I have a correct understanding of how to use my various train/transport reservations. I would appreciate any correction of the info below:

Keisei Skyliner - purchased voucher from Klook, use QR code at electronic ticket machine or airport info counter to get actual ticket. Will the ticket cover the complete fare or will I also need to use an IC card?

Tokyo to Hakone - purchased digital Hakone Free Pass, will activate morning of use; purchased e-Romancecar ticket w/ seat reservation and per email confirmation instructions will print confirmation document. Will I use the Hakone Free Pass to scan myself through the gate at Shinjuku station?

Tokaido Hikari Shinkansen Odawara to Kyoto - retrieve ticket from JR Central electronic machine or ticket office at Odawara station. I bought a reserved seat on a limited express train. Will I be retrieving both a basic fare and a limited express ticket?

Kyoto to Koyasan

• Hoping to take 12:45pm SRS train from Kyoto to Osaka, but it doesn't look like tickets are available to purchase in advance from the JR West website. I'm assuming it's fine to just purchase a basic fare ticket (I will not have luggage) when I get to the station.
• Subway from Osaka to Namba
• Purchased digital Koyasan World Heritage Ticket but made an error and purchased the basic ticket instead of the one with the limited express ticket. Can I purchase the limited express add-on from an e-ticket machine at Namba station?
• The Koyasan World Heritage Ticket didn't have me designate a specific train to or from Koyasan. Will I just activate the pass and use it to get on any train? I'm traveling on weekdays at the end of November. Do I need to be at concerned about getting a seat on overly crowded trains?

I'm slightly nervous about getting around by public transit in Kyoto. I have my Google maps set to prioritizing subway over buses (I read that the subway is easier to navigate than the buses). Sometimes Google maps will give me directions using bus stop names in Japanese characters. Is the best way to navigate that just to screenshot the Google maps directions and then run it through a translation app? Do the buses in Kyoto clearly show what station is coming next? Basically, what is the best way to navigate the buses in Kyoto?

Osaka to KIX: Planning to purchase KATE airport bus ticket. By this point I expect my luggage will have grown a bit (I'm bringing an empty duffle in my carry-on rollerbag) and using a bus sounds easier than trying to manage multiple bags on a train. My hotel runs a shuttle to the Osaka JR station. I plan to stow my luggage in a coin locker for a couple of hours while I do some last-minute souvenir and gift shopping. The bus has pickup locations at Herbis Osaka and Hotel New Hankyu. It looks like latter spot would be the closest to where my luggage will be stored.

Thanks for any input!

Have a great trip! I can't answer most of your questions but I just checked Google maps and clicked on a bus stop near where I stay in Kyoto and all the bus stops came up in English....hope that helps....

You should have the HFP when you get to Odakyu Shinjuku Station. The ticket gets you through the gate (you will figure it out)

about th JR trains:

If you paid the base fare and the reserved seat fee then you will will get both when you scan your QR code

you will put both tickets in the slot at the gate at the same time. The barrier will open and you retrieve whatever tickets it pops out.

that SRS.train is just an ordinary train and you don’t get reserved seats. Just a commuter train and buy at the station and gat on next train

You are asking the right questions which means you will be fine

Thank you @mara and @mrwunrfl!

Have a wonderful trip! Japan and its people are wonderful!

I’m not going to try to answer your questions but we had the best station agent when we picked up the tickets I had reserved on line from Kumamoto to Nagasaki. A slightly complicated trip requiring 3 trains and 5 tickets. The lovely agent sketched out the station changes on the back of the receipt and numbered the order of the tickets we needed to place in the ticket machine!