Engine: I had a 1965 289 stroked to 331 giving me 390 HP and 360 ft-lbs, more than enough for this car.
Trans: I went with the TKO 600, .064 with a 3.54 rear. No problems shifting, smooth as glass. I'd check out the .082 with a 3.31 if you plan any highway driving although I've been happy with the combo I have.
I've driven both the original ERA "Jag" suspension and the new ERA custom one. Personally, I prefer the newer outboard brakes suspension.
Color: I went to several dealers at different times of the day to view colors and see what they looked like in different lighting conditions.
Oil Cooler: not really necessary, but looks cool. Doesn't have to be hooked up.
Roll Bar: I like the single hoop FIA bar, but if you want protection for the passenger, there are several historical pictures of 289's with full width roll bars and IMHO they look alot better than "dual paperclips."
Dash: I personally prefer the "dropped dash." Obviously, that's why I got it.
Wheels: Pin drives, only way to go.
All that said, take all the suggestions with a grain of salt and make it yours!