700r4 and 4l60e are light years ahead of a tf 999 or tf727. if your gonna use the GM motor with the ecm and pin it out, I would have no reservations to use the 4l60e; if you simply looking to run a carb and no computer management, look for the 700r4, they are pretty much exactly the same but the 4l60e is electornically controled. a stand alone management system for one generally runs between $450-$1000 depending on the manufacturer. your np231 should bolt up to either trans.
the only other way to tell the difference is the older 97 after 4l60e was a stronger three piece case, the 1st gen's and 700r4 were one piece cases (look like an elongated TH350