Theoretically, yes. The PTE doghouse is 5/8" taller than stock, is it not? Add a PP and an extra gasket and you're heading towards a full inch.
This helps clear the MAF ducting, pipe, hoses, whatever, but it can play hell with the hood pad.
Tubes, hoses and clamps. I could write a book. Most of the stuff I've seen, from OEM to aftermarket, is of poor fit and quality. PTE sells good hoses - silicone lined, multiple ply NOMEX reinforced. Have them make them up longer than standard. Clamps - well Breeze HD Spring Loaded T-Bolts ain't coming loose any time soon, even on the TB, where the nose is way too short thanks to some idiot designer...