FLHT won't work for rebuilding an FXR.
Lots of changes to the frames year to year, so lots of part numbers. The main things to worry about is the rear master cylinder mount and the steering head stop. With that said, for you it shouldn't be a big deal. Sounds like you'll need trees and forks, so you can go either way, early or late style.
Be aware that you'll need a title for the frame you use and you'll need document the engine as the numbers won't match. Old title transferred to your name will cover that. Also some states get real picky about salvage scooters and mismatching numbers, so check it out before you spend a lot of money.
Lots of used FXR frames out there, but no easy way to see if they are straight. IIWY, I'd be looking for an 88 or later frame and a 39mm front end. Always remember that FXR's share parts with Sportsters. If you ask the price on a Sporty front end, it's one thing, same piece for and FXR is another. FXR's tend to bring a premium price.