I'd go ahead and join the header and muffler the way they are....too long.
The reason ? It's a low RPM, long stroke motor, and doesn't have to be
wound up real tight on the RPM's for break-in.
After you get a few tanks run through it, check the RPM and see if anything
needs to be done. See the head-pipe on this OS RF long stroke engine ?
I never cut the header because the engine was turning exactly what it was
supposed to turn....11,400, with a 12-8 Zinger, on 15% nitro.
See what the engine is doing before you break out the tubing cutter.
FBD.