Re-clocking the turbo is pretty much standard operating procedure.
I didn't care for thr band clamp they supplied that connects the first 2 pieces together. It does not collapse evenly which puts a dent in the slip fit joint. I tossed it after the first try and went with the Walker stainless band clamps. The only drawback with this is it has to be loosened and moved to get to the plugs.
The dump tube is the 2nd piece in the DP chain, The S pipe goes between the dump and the cat.
You'll have to do something with the water supply & return lines since the PTE setup doesn't use them.
Get some stainless allen bolts to secure the exhaust housing to the exhaust manifold. Lube them up good with no-sieze.
You may want to have the DP mounting flange machined to match the exhaust housing outlet. Mine was ok, but not great.
You'll need a different turbo to IC hose since the PTE exhaust housing mounts the turbo in a different location.