Update on my Thunderbolt issue. I spent more time learning about DROM and SSDT. After noticing my root port didn't match the expected 21 for the Titan Ridge card. I moved the card to the bottom PCI-E slot instead of being in the middle. I think this changed everything for me. Both Buses are showing, I enabled the SSDTs for both (RP5 for vision and RP 21 for Titan Ridge card) and now things seem to work really well. All of my Thunderbolt devices are showing, and were able to be plugged in while the system was on. I might have been able to make some edits to the Titan Ridge DROM to match it to the other slot (It was PEG1,1 I think) this move of the card seems to be much more stable.
Thanks again
@CaseySJ, if any of my experience can be helpful to others, I'm happy to check/confirm anything for you.