RE: engine rebuild
Did you compare the new parts to the old ones to make sure they was the correct parts to start with?
Theres no way a piston can only go up 3/4ths of the way and get enough compression to fire.A 2 stroke engine has to have good compression to be able to run.
As far as the ports go I line them up, so if the hole in the sleeve is smaller I split the diff on both sides of the exhaust port and so far I have not had a problem.
I agree a trip to Mecoa may be your best bet here.