Sounds like an awesome trip!
If you plan to do the whole Souya- to Sata-misaki thing then I would say 5-6 weeks is too rushed especially if you are new to bike touring. I did almost the whole thing in 2005 in 6 weeks and it felt very rushed. We were trying to fit the schedule of someone who didn't have a lot of time available and then she dropped out after a week because of knee pain due to lack of cycling experience (she was young and reasonably fit too but her only biking experience was 5km to school and back each day). We had a lot of days over 100km and we did virtually no sightseeing, just riding. Using the 18 kippu will help a lot but remember they aren't valid until about July 20th.
Rentals are essentially non-existant for touring in Japan. I've only heard of rentals being available to people on expensive guided tours. You may find it difficult to buy a bike for your size in any store in Japan without special ordering it. You'd have a pretty tough time selling it afterwards as well but I would guess your best bet is to connect with US bases in Okinawa.
Minimal basic bike knowledge would be patching an inner tube, changing a set of brakes (you'll probably need to do that twice), and doing the breakdown for putting your bike into a rinkou when taking the train.
Get a touring bike not a mountain bike or a racing style bike. SPD pedals and bike shoes will increase efficiency but if you aren't used to them you will likely have an accident.
The Japan Sea coast of Touhoku is much flatter but I would recommend doing the Pacific Coast to see the tsunami zone and help rebuilding efforts by patronizing local ryokan/minshuku (and I'd recommend volunteering a few days). Shikoku doesn't appear on your list but I would highly recommend it. I've heard the ferry from Atsumi-hantou to Toba is running again so it's easy to skip Nagoya.
You can see my Touhoku tour journals here:http://www.crazyguyonabike.com/katakanadian