Just going through the manual there looks to be a few other settings that should be changed also;
Limit CPUID Max. to 3 - Allows you to determine whether to limit CPUID maximum value. Set this item to Disabled for Windows XP operating system; set this item to Enabled for legacy operating system such as Windows NT4.0. (Default: Disabled). Now set to Enabled
HPET Support - Enables or disables High Precision Event Timer (HPET) for Windows® Vista® operating system. (Default: Enabled). Now set to Disabled
MS-DOS prompts - Definitely doesn't come up smooth. There is a split second after running cmd where there is some distortion or some artifacts appear on screen. I did some testing within Windows and found that Duke Nukum 1 gave a black screen but sounded like it was working in the background. I was able to end the task and get be to the desktop easily. I can also tab away and then back to the game to make everything run fine. Duke Nukem 3D was working without problems. Now when launching cmd in 16-bit colours the colours go out of control and look crazy. No problem launching cmd with 32-bit colours.
Restart in MS-DOS Mode - Windows protection error
Phantom Floppy - Legacy USB storage detect was already disabled. But I enabled it and the floppy drive is now gone.
By now I'm getting explorer crashing, active desktop crashing, icons on the desktop are staying selected when they shouldn't be. I've reinstalled Internet Explorer and the U98SESP3 main updates but the issues persist. Tried formatting the disk and starting again with setup /p j and reached approximately the same point. The only device manager ! is a resource conflict with a motherboard resources device. It's still very fussy with shutdowns especially if some new drivers or software has been installed. Restarting in MS-DOS mode will not happen but I can boot into it with F8. Normal shut downs work as expected from both the start menu and the power button. Duke games behave the same way. It feels a bit like my GPU or monitor just doesn't like old fashioned resolutions. Hopefully I can try another monitor tomorrow.
Are changes related to ACPI and AHCI for that matter useful for performance or just to make everything work? If windows supports ACPI and my motherboard supports ACPI, then installing with /p j should be the correct way?