Don't bother with headers. I did LT's and spent 3 months chasing CEL and codes trying to trick the system into thinking the front cats were still there.
IIRC I looked at shorties and they involved cutting the front cat off the OEM manifold and welding them back to the shorties. I'm no expert at welding so I asked a couple shops about it, not a single one would touch it. Not enough room to properly weld with headers attached to the engine, and trying to do it off the truck means the angle probably won't be correct which means misalignment with the Y-pipe.
Skip the headers, if you're looking for a better flowing exhaust grab URD's Y-pipe. It will remove the restriction where the driver's side gets reduced down going under the transfer case.
Intake is your call, but the TRD box doesn't add anything and still draws air through the same size hole in the inner fender. If you're thinking you want more air then look at something like the aFe MomentumGT CAI (ProDry-S means no oiling filters). I had that exact CAI both with and without URD's MAF Calibrator. Without the MAF Calibrator it was a little extra noise, and maybe a little better. Add the MAF calibrator and it was a much peppier experience driving the truck. For noise can always put the plug into the extra air intake port on the air box and quiet it down, though it does lose some performance when you do so. I also switched to 91+ octane right before I installed the MAF Calibrator.
