sounds like your "break in" is about right ..altho I would consider (if you haven't already)checking the trans oil for any signs of coolant before you get started...if any coolant in oil,it does have a bad w/pump seal ..
also was there any signs of coolant in the cylinder or on plug before the rebuild?..if any coolant it maybe had a bad head gasket ..
for break in I would consider going up at least size on main jet ...
also be sure to use plenty of 2 stroke oil on parts/cylinder /piston while assembling it
& have a few plugs on hand in case they become fouled at start up ..
better to foul plugs than ruin a new top end
keep the radiator cap off the first time or 2 to make sure you have coolant moving /flowing in the system ..& see if when you rev the motor the coolant moves
a lil faster & slows when you let off throttle