You want your
oil pan and bellhousing to be roughly the same low spot on your car. Trim if necessary, but don't let the bellhousing sit significantly lower than the pan. With a mild 289 stroker, you may consider the TKO 500 as well. It might be smoother to shift. I just LOVE the old TKO in my FIA, but that transmission is no longer available. Sounds like you might want the 4 speed shifter ball, which is a nice touch - even on the 5 speed for the authenticity you are seeking. It also confuses people who attempt to drive your car when they look at the shift pattern and can't get it into reverse (:
Your next consideration is which gear ratios you want for the transmission and rear. Let the debate begin. Lot's of factors to consider (tire size, engine torque curve, driving style, anticipated touring miles on the highways, etc...) Or you could just say the hell with it and choose the 3.31:1 rear and get a Toploader mated to a rev happy engine like the stock HiPo was/is.