If the engine came with Drive By Wire (DBW), you will not be able to use a Drive By Cable (DBC) throttle body on it. The problem is threefold:
- Crank position sensor of the wrong type (Passenger side, above the starter. The 5.3 should have a gray one in it.)
- Crank reluctor wheel of the wrong type (58x v 24x)
- The ECM will be of the wrong type for one or the other.
If any of these things are out of whack, the engine won't run, to include the Engine Control Module (ECM) whether you get it flashed or not. If you bought an ECM which is made for a DBC system, it won't work with the 58x reluctor wheel engine. If you have an ECM which is for the 58x reluctor, it won't run with the DBC throttle body.
There is a way around the 58x v 24x reluctor debacle. There's a conversion kit you can purchase from Lingenfelter Performance Parts. There's a good write up of it in Super Chevy Magazine, where the guy put an Gen IV LS3 into his Gen III LS1 equiped Z28. The box from LPP makes the conversion so you can run the DBC throttle body on the 58x equipped engine.
As for the LS1 injectors, they should be able to run in the truck manifold, but if you have an LS1 manifold which will fit the cathedral intake ports, I'd use it because it will flow better. I doubt the LS1 rails would work on the truck manifold, though that would be easy enough to check.
As for Active Fuel Management (AFM), if the engine was running good without mechanical issues (AFM lifters tend to go bad) or valvetrain noise, you can simply have it programmed out of the ECM. The engine will continue to run correctly without issue with all of the AFM parts in place. The engine just won't be using those parts to put the engine into AFM mode (which, from my understanding, there's a very narrow window of operation for AFM anyway). If you plan on putting a new cam into the engine and not include the AFM, you'll want to replace the lifters and remove the other AFM goodies, as well as getting a new tune to get rid of it all together in the ECM. Here is a page of a guy who does this programming for a living. It appears there's a lot of good information on the page, though realize the guy is trying to sell you something, so be aware. (I've paraphrased the needed information here, though.)