There are lots of really smart folks here, but the problem seems to be the distance between you and others that are familiar with your system....
Before tearing it out, I would reach out to those tuners who are familiar with the system that is on the car.......try to make it work.
When making wholesale changes to the car, you will end up with wholesale problems. Lots and lots of wholesale problems to work out, some that may be beyond your experience, or not.
Correcting most of those issues on your own..... or by paying a real professional to sort it out, seems to be the direction this is heading.
Don't be afraid, the fact is, if you don't want to spend RETAIL, BIG, BIG money to fix your self imposed problem by changing what you have, you need to be ready to pay to have some other person get your car squared away.
Then again, you might be an absolute genius with these little TR's and I could be completely wrong.