if your changing the engine and trans you will need to change the computer anyway. and for that computer (PCM) to work with your interior computer (BCM) the vins will need to match... this will require tuning anyway. so you might as well pic the engine and trans you want and have the pcm tuned to match. there are mail order vendors who will sell you a pcm or you can ask around and find someone local to tune your car.
I also agree with going with the non GTP trans. when i did my swap from the original 3.4L DOHC engine to a 3800 series engine i did this. i chose the regular 4t65e and also go the L36 and got a topswap kit. the non HD trans gives a gear ratio that allows faster acceleration and using the higher compression L36 will give me more power for the same boost level once i install the topswap.
from the sound of it all though... you are considering changing the engine for a more reliable one. in this case go with the L32 and call it a day. for mods it all depends on how fast you want it, but i would start with headers as now is the time if the engine will be out of the car. Now is also the time for a cam if your plans all for it in the future. but i just dont see getting a diff engine only to crack it all open to drop in a cam... might as well cam your existing engine and do a gen V topswap.
