I will eventually go with a bigger alternator but the little tiny stock dude is still hanging in there. Not sure if the CS144 or if a bigger Nippondenso, though the former certainly beats what output I'd find on the latter for the price. CS144 also makes more sense because they're easier to find, I guess.
I've sort of looked into this for a future mod...iirc, the upper bracket remains where it is, right? The stock alternator currently sits 99.85% under the dual boxes, wouldn't the GM alt do the same? As long as the upper GM mounting ear is long enough to compensate for the angle from the lower bracket (I'm assuming there is one, I don't know for sure) then it should fit under the battery box. Right?
I found this interesting...
http://www.toyota-4runner.org/3rd-gen-t4rs/135318-docs-cs144-alternator-upgrade.html
One of the guys later in the thread mentions the alternator hitting his oversized filter...I don't know if he means something taller like the v8 filter or? I didn't think about that aspect of the gm vs yota alternator.
That's probably more musing than you were looking for....now I get to sit back and see what you come up with and if you really can fit a GM alt under the batteries.