jjones,
First, it's far more important that the engine is straight up and down (vertical) than that the lever is. Second, if the engine is indeed vertical, the shift lever should also be vertical. If it's not, something is amiss. MGA shifters are straight up and down in neutral.
We do this conversion in our shop quite regularly. In fact, we have two going on right now, though we use an MGB engine and gearbox or MGB engine with a five speed conversion, the basics are the same. By the way, Dick mentions the water outlet/inlet situation. We have a radiator shop close up the stock openings in the TD radiator and cut in new ones to suit the MGB (or A) engine. Then we just get some rad hoses with sections of right angle to suit. Nifty.
Motorbill
From Lola to Land Rover, If it's British and has wheels, it's likely I've bloodied me knuckles thereupon