Long story short I ended up converting from MBR to GPT by manually deleting the MBR partition and creating an EFI partition. Then due to some free space issues I used gparted to shift that free space back to the system partition, ran a disk check afterward and corrected any errors. Also ran /scannow and fixed a few files.
- The system boots fine
- Motherboard is set to EUFI only
- Secure boot is disabled
- I have tried several bootrec commands with no luck
- I am unable to get into safe mode with F8 during boot
I suspect there is a registry key or something that I am missing that will tell msconfig where the boot files actually are.
Interestingly if I move from AHCI to RAID I get errors regarding the BCD and windows won't boot. I'm not sure exactly what to make of that.