that's a good question...if ya use the 44, ya get the benefit of lower torque/stress on the new parts. if you use the 36, i'd suggest a lot of pedaling to take the initial load off when letting the clutch out, but then you'd have the benefit of a bit more speed while still laying-low during the break-in. engine rpm and stress are the crucial factors. use your discretion when choosing, & base your choice on your riding style and amount of mechanical experience.
my opinion: if you're "just" a beginner, stay with the 44 and only do 20mph tops for the first coupla tanks. if you understand the gist of the above disjointed rambling, then go with the 36, saves a re-install later 8)
yea use the 44t its alot smoother on the motor, because you have to keep your speed down to about 15 20 mph during break in. the 36tooth sproket makes the motor sputter more on lower speeds. put the 36tooth on after you break in the motor and get a better feel for the bike.
it seems like its going to be a hassle but it will be worth it in the longer run when your bike is broken in and your getting high speeds because your motor is working smoothly.
I have a 50 tooth that i like to use for break in purposes then swap down to the 44...
I don't mind changing the sprocket, I just throw on the tunes and start wrenching.
I made a sprocket truing stand from an old 39 Elgin fork that the steer tube was thrashed, a piece of plate steel, and a chunk of bar stock.
I wlded the forks to the plate, then welded the bar stock on the underside of the plate. I can then clamp it in my bench vise, set up my dial indicator with mag. base and really dial in the sprocket this way.
Works well and is pretty low buck.