Sorry, IDK much about tuning. I know your code reader isn't going to do anything, you'd know, if it could, because it would be a lot more expensive than other code readers and have "You can do tuning with this" all over the packaging.
The main problem for you is that you have a frankenstein truck, that you don't know exactly what's been done to it.
From what little I know about it, you need to start with figuring out what computer systems are in there running the engine and transmission, as it's my understanding you either need to use a different computer from what's normally used in gmt800's to run the engine because the reluctor wheel in the gen iv engine is different from gen iii's, or he took apart the engine and changed the reluctor wheel to what is used by gen iii's (and probably need to change other bits as well).
You might also verify:
-injector p/n's (either directly with an inspection camera or pull one to verify it) to see what's in there
-check casting numbers and/or labels on the head to verify what they are
-possibly pull a valve cover and use a dial indicator to check how much intake/exhaust valve lift you are getting, to see what cam is in it
-maybe use live data and examine the downstream o2 sensors to see if the cat's are still in working order (some people will punch them out, and then put spacers on the sensors so they don't read correctly, or put dohickeys on the connector to act as fake sensors
Once you've figured that stuff out, then perhaps contact someone like blackbearperformance.com, they seem to have a good reputation (this is not a recommendation of them, just a name I've heard over the years that other people are happy with, there are other good tuners as well, I just can't come up with any other names at the moment), and see what they say about what kind of tune you need and how to get it into your computer.