Biggest headache I see is that your engine is a 2005 and the truck is a 99. You can use a 2005 PCM, assuming you have all the DBW parts you need, but the BCM and the rest of the serial devices in the truck won't like it. AC request becomes a problem.
Motor mounts and stands for the frame, trans crossmember, driveshaft yoke and length. 2005 engine will also have a returnless fuel rail. You could use a vette filter/regulator to adapt your fuel system to the newer engine (tuner needs to know this (non-referenced regulator)).

Even though you have the engine and trans, don't expect it to be cheap.