Unfortunately I really don't know how to help you. Interesting conversion, I'd never heard of it being done. Pardon my ignorance but what is the benefit? Wouldn't really throw a stronger spark so I assume the cdi box has different timing curve?
Back to the original question..... If you are converting your entire system then it will need to recognize the TPS settings(I hate tps), if not you will have issues. I again am unsure if you can 'fool' the cdi box into thinking tps is set at a certain perameter. So while I may have spewed a bunch of crap, I didn't really help at all lol. Sorry, hopefully someone can chime in with more knowledge with TPS.