I wish I could be of more help, but I jumped on the manual bandwagon with my swap.
I will say this though, if the engine is to remain stock, I see no reason to the transmission (that cam with the 3.4) should need to change. now if the plan is to start modding it, you have 2 options, there are companies making parts for the 4t45e, so you could rebuild it with beefier internals, or you could swap to a 4t65e, or you could do the manual thing. the 3rd if probably the most involved, but IMO yields the best results.
Drivers side, use the stock fiero axle you took out. The passenger side, IF you are Not using a 4t65e-HD, the stock axle "may" work as well. I used a 4t65e-HD, so I had to have an axle built because on the Heavy Duty trans, the pass side axle is about 20% larger in diameter than the stock axle. so a 'Stub" from a HD trans is coupled to a Fiero axle.
Thanks for the suggestions. We have the transmission (4t44e) centered and are using two drivers side stock th125 axles.We have had both axles come out of the transmission while driving. I think axles one inch longer would solve the problem. We do not have a build thread,but we do have some pictures to post when we get around to it.