Paul,
Looks like you are close for either of two choices. One is to adjust the cowl and fuse depth to just cover the header, the pipe connector could allow the tail of the pipe to tuck into the aft fuse close to the wing. Second option is as Randy said get a header with less rise. Before you change things I would connect the pipe and see how it laid out. Once you have a rear mount selected you can complete the fuse design.
One thing to consider, try to keep the pipe as low to the wing as possible to keep the vertical CG closer to the wing centerline. This avoids having the ship roll in from the low VCG. This has been one of the issues that takes some trim skills as both the engine torque and the low VCG team up to roll the ship in (assuming a counter clockwise setup). A reverse clockwise running engine would really help this, but I have not seen any mods available for the PA's (or other stunt engines, OK except the Fox 35 - there is a reverse crankshaft for it).
Best, DennisT