I'm absolutely no expert on this but I'm fitting my ball-screws at the moment so I'm sharing the LITTLE bit of experience I have.

1) I went the other way round and ordered it ball park and then worked around that but I think your way is better. I might stand corrected on this but there's normally a little circlip on the floating end of the screw that serves little purpose in my mind. If that is not used you do have a few mm to play with so rather err on the short side, the shaft will just sit a bit shallower in the floating bearing which I believe is not a problem.

2) I went for the standard machining and the bit that sticks out on the fixed end after the lock nut is in place is a bit short for my liking. I'm not familiar with that motor housing so I have no idea about the correct F length. Keep in mind that with most of these flexible couplings you do have a few mm to work with both on the motor and shaft side so you will likely be ok if you just work it out as best you can and order it that length. Assuming its 12 or 16mm dia skrew and you really want to play is super safe then go a bit on the long side and cut any excess off with an angle grinder or even a dremel tool with one of those clip-on cutting disks will cut it off in no time. It does not have to be cut off perfectly square.

3) I've never used the supported rail so I can't be of any help there but I think it might be risky to make assumptions around where those hole are on non standard or even standard lengths. These rail type products are often made in longer lengths an then the reseller cut them to your requirements so a lot depends on the guy who's doing the cutting :-) Those holes do seem quite far apart so why not just drill your own holes where you need them?