Are there any special items (problems) I should be looking for, when I look at a donor motor and transmission? The combo is 2004 GTO.

2004 gto = ls2

I thought 2004 = LS1, 2005-06 = LS2

The '04 is an LS1. After that LS2.

The '04 uses an F-body accessory drive. Overall they are pretty nice. Prices for LS1 are lower than LS2. LS2 had drive-by-wire capability. Look for the standard stuff like you would for any engine. There are really no glaring problems with the later LS1 engines.

One advantage of the the GTO is that the engine harness is long enough to mount the ECM in the front LH fenderwell.

Get everything that you can. Fasteners, clips, lines, ECM and harnesses, etc. It all adds up in a hurry. There's some info and pics on my website.