Studied intake system again. I will need to remove and re glass the back of the right plenum to facilitate clearance with the #1 exhaust pipe. Apparently, the exhaust that Showplanes designed around is no longer available, and the Custom Aircraft exhaust is a bit different.
It also looks as if the fit of the intake plenums is not as bad as I thought. It will work but I will need to replace the plenums that are now too short.
Remove lower cowl.
Trim and smooth lower aft fairing.
Install lower aft fairing and verify fit.
Temporarily install #1, #3, #2 exhaust pipes. Verify fit of heater muffs. The #3 muff looks like it will work fine. the #2, I need to do some research on. I need to find out where the scat tubing vent is located on the baffling to determine if the muff will work.