Most of us just use the OEM one as it came. My motorset came with an SR tranny. I installed the motorset and found out the tranny was a no go. So I took it out and swapped bellhousings with the KA one from the old motor.
KA trannys are relatively cheap and easy to find, so I don't really see a reason to go rebuilding it. I'm not sure how expensive it can be, but I suppose you could go that route and get it done.
FYI: I did an OEM rebuild as well for reliability, Replacing the tranny/bellhousing will only take a day if it were to crap out on you. I also daily this car.
_Allen
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