I have used metal pushrods for throttle and choke with the servos mounted at the bottom of the motor box without issue
That's not a good idea, as any metal can conduct RFI. You may get away with it, but nyrod is better.
Carlos, it looks like you have an older BME twin there with a CH ignition that has braided ground straps that attach to the cylinders. Those grounds have to be good. Try hitting the connection with an OHM meter and see what resistance you have. Do you have resistor plugs in the engine? Maybe a newer ignition with shielded wires and caps would be a consideration?
Exactly. Good caps & ground straps will fix most RF-caused glitching. (Not picking on you, SR&T, you have probably seen more installs than most.)
I've seen folks go to PCM, separate channels/receivers, and 2.4Ghz setups trying to mask glitching. If you fix it at the source (shielding the plug & wire), you'll find 99% of the troubles go away.