there is nothing wrong with rebuilding your own auto transmission either. As long as you get a good service manual for your tranny, it is really quite straight forward. You just have to READ EVERYTHING before you start.
If you don't want to rebuild your own, like it was said before, you will PREFER a 95 or 96, but an older e40d will work. The newer ones have some updates that fixed some problems that caused premature failure problems.
If I were you I would spend the cash and get a reman. You will be looking at about $2000 but it will have a warranty and have some additional upgrades that will make it last longer.
If you want to swap to a c-6 (because you don't need OD) then there is nothing wrong with that, just make sure that you do your research on the swap first so you know what you need to do. If i remember correctly, it isn't a direct bolt on. You may want to add up the prices of what you need to do the swap to see if it is actually cheaper than a reman e40d.