Sounds to me like a stuck roller in the CVT system.
Before we get into checking this, here's a few tests you might want to do.
1 - Check engine PSI. For a stock piston / head replacement, the PSI is probably around the 100-120 range. The Pred-90 is 120 PSI - fresh stock. Pred-90 normal PSI is 100. I'm sure the stock E-Ton 90 2 stoke is the same PSI range.
2 - Did you only change the piston / cylinder or did you also change the air filter system? If you changed the air filter system at the same time, you definately need to re-jet.
3 - Perform a "quick check" for proper jetting and low RPM Air Leaks. This can be done by looking at the spark plug color. It should be slight black to beer bottle brown at idle and at the 1/4 throttle range. Let the engine idle for 5 minutes and check its plug color. If it isn't within this color range, it could be an air leak, dirt in the carb or its air screw or lower size jet may need to be adjusted. If the plug is white or has white specs, stop running it. The engine is way too lean and thus, running too hot.
Note: To learn more about testing for air leaks (especially after upgrading a 2 stroke engine), surf: http://atv.off-road.com/atv/article/....jsp?id=190479
4 - The problem you described is most often a stuck roller in the CVT system. Especially if it worked great before your engine re-build. To check for a stuck roller, you need to remove the CVT cover and remove the front clutch system. For more details and pictures of this area, surf:
Note: When testing a rebuilt engine, I've been told many times that it is recommended NOT to place the ATV on blocks and "punch its throttle". With no drag on its rear wheels, the CVT system revs "super fast" very quickly and sometimes, its CVT rollers get stuck. If testing on blocks, press the gas slow up to 1/2 throttle and let it rev down at its natural speed. Thus, the CVT system isn't "jerked above" its expected normal operating stess levels.
Hope this info helps...