Assuming that your old cylinders were .100 over and your new cylinders are 64mm and you didnt change the domes size this could be the route of your problems. With the new cylinders being smaller you will have a smaller combustion area and more compression also did your old cylinders have any porting done to them? This would cause lower compression before and allow you to run this setup with pump gas. Right now you are way over the limit of safely running pump gas with your compression/timing combo. Sounds like to me and this is just my $.02 that you just have to much compression and timing for pump gas, keep in mind that there are many different varibles that can effect your compression like bore size, porting, squish, base gaskets, and how fresh the motor is just to name a few. This may be why you were okay before and not now, try lowering the compression by putting in a larger size dome and i would also consider getting the dome custom cut to fit your motor cause it sounds like your squish is a tad loose or you might try a thinner base gasket if available.
Just my $.02
Andy
M&M ATV