You have already proved its not the ignition, by the bypass, its the Emcotec whatever that is, I just use an ordinary HD switch and set up the engine so that at low throttle trim the engine cuts, if you need an on board ignition cut due to local rules, then put a servo on a manual switch, gets rid of extra electronics that can and in your case did go wrong. All of this is only my opinion and will be dissagreed with by all those who use opto isolators.

Mike