Given the ratio of reverse gear you will have to run the electric motor pretty fast to get up to highway speeds. Also you will be running the ring and pinion on the back side which is not good for longevity. Look for a 996 transmission. About the same size as the 01E and would work better.
Part of the issue is the throttle body is at the back of the intake manifold and gets in the way of doing a bundle of snakes type header system. I did headers for someone building a GT40 here in TX and that is why we went with more conventional design.
The '99-'04 Boxster S 6-speed is probably about your best bet considering money spent for strength. The Audi 01X is another pretty good choice if you aren't planning too much HP. The Boxster has the advantage of already having cable shift designed on it so no additional linkage is necessary.