You will not like my suggestions, but they are based on experience.
1. Replace lipos and regulator with a 5 cell NiCad or NiMh or 2SA123-2300 battery going JUST through the JR HD switches on the RX.
2. Replace the lipo and Jomar optical kill (bypass all that crap) with just a REGULAR 4 or 5 cell NiCad/NiMh or 2SA123
3. Don't change anything else.
4. Run the engine. Do everything you can to make it act up.
5. Observe that all problems are gone.
6. Beginning with the ignition stuff, replace ONE piece of your original stuff, one at a time, until the problem reappears.

(You will find the Jomar and the MPI regulators need to be put in the round bin)