Man, oh, man.
Hopefully, the issues are sorted out.
I can’t help but think with so many changing variables co-occurring that it’s going to be challenging to pinpoint a singular culprit. Downpipes are going in, intercooler changing, exhaust, boostane, and mystery marathon 93. That’s a lot going on to add to the tune, maybe not being suited to all the modifications since the tune came first.
Everyone’s approach to addressing the problems will differ, but if the tune purchased was set up for an otherwise stock car then I would take the path of leaving it stock and figuring out the problems with the tune without introducing additional variables. It’s at least worth another baseline test with the stock ECU. It could be something as minor or as pulling the plugs and verifying their gap. Yes, I know it has been stated here that they don’t need to be gapped for this tune, but gapping isn’t tune specific for this platform. Once that variable is eliminated, then you’re only left with one possible culprit, the ECU tune, and you can work with them to address the issues and inform them of your planned modifications to take into account for a potential reflash.
Every once in a while, with these one size, fits all tunes, there will be inevitable issues. I’m glad you had the JB4 and were smart enough to grab some early logs before things potentially turned catastrophic.