Ignition or Carb problem

I bought an Avid MK IV with a Rotax 912UL. The engine was off of the airplane do to having engine mount crack repaired. Both carbs were sent off and rebuilt at this time. I installed the engine on the airplane with new charging coils, new ignition trigger coil assembly, new NGK sparkplugs, 2 new carb to intake rubber connectors. The engine ran OK with the carbs sync'ed. After the first flight I noticed it was running a little rough when I pilled back power for landing. After I was on the ground I did a right and left "MAG" ignition check and noticed that the engine died when the left switch was turned off. I replace both CDI boxes with the ignitech units. The The carbs sync good ay 2200 and 3500 RPM's. The engine still has that rough idle and after a short flight around the airport, Its starts to have a miss. Could this be a coil going bad or do I need to check the floats in the freshly overhauled carbs? Another thing that is strange is that when testing the ignition switches with the sparkplugs out, so I can see the spark, The right switch in the "ON" position gives spark to 3T, 4T, 1B, 2B, and, 3B. The left switch in the "ON" position gives spark to 1T, 2T, and 4B. Could a coil have a crack or an sparkplug wire be bad letting 3B get power from the other switch.