Sorry you'll have to reinstall. You might get away with just reinstalling RR/RC, but if that doesn't work you'll need to do a full reinstall of SS.
No to have both installed you're going to have to have two copies as you described.
Yes but you will get the supply system back as BftB2 has it's own traits file that will overwrite the no-supply file.
Crimson Tide works fine. Been using it myself and I highly recommend it
The checkboxes when you install 6.1 dont really matter as the BftB will overwrite all the files any of those submods use anyway (except for permanent arrows). But to be sure they should be left blank as BftB isn't designed to work with them yet (again, the permanent arrows should still work fine though)