1. I've never heard of this and don't see how this could be the case.
2. Not sure what you're describing
3. Sounds like you have some electrical gremlins that need to be worked on.
4. You learn to live with it. There is no fix because nothing is wrong.
5. Please use another word to describe what's happening. I can't understand what you're describing.
I would have someone get rid of that stage 2 tune ASAP or get a turboback/downpipe. Do not put it off. Your EGTs are probably sky high and that new motor may start running into issues.