Sounds like you have changed part of the ignition, so to save alot of guessing and part swapping you should have the rest tested. It doesn't have to be a marine engine shop - any place that works on 2 strokes will have the necessary gear to test your stator and trigger. That will determine if it's an "ignition miss" or a "lean sneeze".
If the ignition is ok, then a few different gaskets can cause a lean sneeze. The most common would be gasket between the carb and the manifold - the manifold gasket itself or the pair that sandwich the reed cages - also the powerhead base gasket.
However, from what you describe it sounds like maybe you have a problem with your low speed bobbins on the stator (assume you have a non-cdm ignition since you mention changing the coils). The low speed coils provide pretty much all the power below about 3500 rpms after which the high speed coils kick in as well. But like I said, have it tested. A new stator for the 3 cylinder model (if that's what you have) lists in the $375-500 range depending on the exact model...