I have optional header and pipe, so nothing to say there...
The hole in the cylinder; I matched the threads to a short bolt about 1/2 long and Loc-tited it in there.
The gear box breather I couldn't figure out, so I just cut the hose and used that black high-temp silicone to hold the properly sized bolt in there. Eh- what the heck. It looks OK...
Engines are shipped with plugs blocking everything. I got one just the right size to cap the nub on the carb. That's a tough one though. Tractor Supply might have something. Otherwise call around to mechanics to see if you can get any they take off of engines they get in.
All this includes removal of the yuck can under the seat, of course.