Stock 5.3L heads flow very poorly and I wouldn't even consider using them on a 6.0 without having them worked.
As far as the engines, they are a direct swap as long as you have a 4.8 or a 5.3L. Make sure you have a Gen III engine rather than a Gen IV engine. They have different reluctor wheels and the cam position sensor is in the front on the newer engines.
As far as the transmissions. It is a fairly easy swap. The hardest part is the transmission crossmember. If you have a 99-early 2000 truck the crossmember is extremely easy to modify. If you have a 2000.5-2006 then you'll need to section it and move the mount back about 6"(it may be more or less, I forget).
The wiring harness can be altered fairly easy by switching a few wires here and there.
You can even use the factory driveshaft on the 2wd truck but you'll need to modify the yolk at the differential.
There's a few more little things here and there, but that's pretty much the basics of it. The engine swap is the easy part, an the transmission swap is a bit more involved but certainly do-able.
