A little suggestion before you bolt the engine to the frame, let it pivot on the swingarm bolt until you get the pipe on.
That way you can move the engine around as you're installing the pipe, and once the pipe is mounted up you can install the engine bolts.
It was the only way I could install the 250 Q pipe in my frame (no clearance at all) and it simplifies things on hybrids and zillas if you have any clearance issues.
You can install the pipe while the engine is bolted down (obviously), but being able to move the pipe helps installation, and it's not like you're doing any more work than you normally would.