I'm afraid I don't have the answer, but I think it's a very good question. I'd never really thought about the nature of the file that is created when using takes. But if, as you say, it creates just one big long file, you would think REAPER would add some kind of start point and end point data. I'm pretty sure WAVs can store loop point data, but it's whether they can store multiple ones.

msquared, it's worth trying to place the takes on adjacent tracks, time-aligning them and then imploding them into takes. -select them, Right-Click, <Takes>, <Implode items accross tracks into takes>. They should possibly then be in the right position time-wise and you can try to remember or work out anew what your best takes were. Any help? >

sorry i cant add anything, but I would definitely try this ^ first.