Somebody feel free to correct me if I'm wrong, but to the best of my knowledge, here is what I can tell you:

1. None that I know of. ITR is probably your best choice (unless you want to go with an older cable tranny, which I don't recommend). Don't forget you also have an option of swapping shorter gear sets, if you really want shorter gearing (quite pricey, though).
2. We don't have any of those trims here, but all b-series trannies will bolt on. The only thing you need to worry about is the older trannies, which are cable trannies. You should stick with a hydro tranny to save alot of headaches
3. In some cases, yes (depends which tranny you decide to get), but I don't think you'll have a problem using the ITR tranny. I believe the CV shafts are interchangeable.
4. The flywheel follows the engine, and the clutch follows the tranny.

Again, i'm not 100% positive on everything, but if somebody notices any mis-information, please feel free to step in a set me straight