Remember - if you get bored with your 390, you can use most if not all the stuff to bolt onto a 427-428.
Another option: -- if have a talented machine shop near by, you could put a 428 crank in your 390 (possibly new pistons due to height of piston pins) and have a 410 for not a whole lot of cash outlay.
390s can run well and in a light car (even a heavy cobra is tonnes lighter than a galaxie was) you can jam down the road quite well.
FEs are a special beast and can be a pain to sort out correctly , so I would read up on 390s and make some new FE friends to help you out--and you should be fine.
Gears: There is a Short shaft 10 spline Tremec TKO 500 that should bolt to the top loader housing and with a small drive shaft mod. -- then you can have a 5 speed
--Steve