They will do all of the rooms, yes. Last time the process took about 6 months for FQ, but I guess it might be a bit quicker this time if they are not doing doing quite such a major refit.
Yes, there is an internal shuttle bus, which is also the Disney Springs bus, and also some of the other bus routes share a times too (mostly that would be in the FQ to Riverside direction, so ask the driver first). The boats call at both resorts until around 5pm, after which they run as independent services.
International guests don't get their Magic Bands posted to them, which means you have to pick them up at the front desk when you arrive, and and you won't have the option of direct-to-room checkin unless you still have working bands from a previous trip and opt to use those again. However there is no disadvantage to doing Online Checkin, so I would suggest doing it anyway to cut down on your time at the front desk as your credit card, PIN, etc will already be set up. Also you might stand a slightly better chance of getting your room requests as they normally assign you a room an hour or two before the arrival time stated in your OLCI - which means that if you don't like what they've initially chosen, you can ask them to check again at the desk and there may be some different Ready Rooms to choose from.
Andre