Almost all the trucks use the same PCM that is in the 99-02 f-body, just get one after 99, they used it in about every LS based V8 until 02-03 and in some of the trucks until 08, this is the computer to get as there are custom operating systems and lots of options for tuning these, however all of GM's V8 PCMs are tunable so it isn't detrimental.
The only major difference between a 4.8 and 5.3 is the crank, the block is the same part number betweeen them. These engines have the smallest bore diameter of any LS engine so you have to watch what heads you swap onto it, but if it will work on a LS1 (LS1 is only slightly larger, about .100") it will work on one of these. When you start talking about 6.0L and bigger displacemnt the cylinders get bigger and all GM's heads interchange. Starting in 04 the V8s starting going to different crank and cam reluctors, different knock sensor locations, and a few other minor changes, these starting getting called the gen 4 V8, requires a different PCM but depending on build any of these parts can be interchanged it just depends on how deep you want to go. If you have specific questions I'm sure i can answer them.
As for transmissions the bolt pattern is close to the old SBC but only about half the bolts line up, the top of the bellhousing bolts are different. I know guys are using this stuff but I don't have any more first hand knowelege then that.