Dual Boot Win 7 Ultimate x64 issues

Please post back a screenshot of your maximized Disk Mgmt drive map with listings, using Snipping Tool in Start Menu. Label what is on each partition.

Confirm that you are receiving auto-disk check at boot on each HD.

Your HD's are not independent but are booting off of the one System partition on Disk0 - as shown by it being the only one marked System.

To correct this unplug Disk0, boot the Win7 DVD to run Startup Repair 3 Separate Times
on Disk1 to write the System boot files to its SysReserved partition which is already marked Active and correct any Startup issues triggering repair loop.

Once it starts on it's own by setting it first to boot in BIOS setup after DVD drive, or using one-time BIOS Boot Menu key, reboot several times to make sure the autoStartup Repair is not still looping.

If not, plug back in the other HD and see how it runs. If either still loop into Repair unplug Disk 1 to run the same Repairs on it while the other HD is not plugged in.

OK Ill try that and let you know how it goes. But some info I didn't mention which may be part of the issue or help my cause:
Disk 1 was my original Win7 install before changing my MOB and CPU.
Disk 0 was my original Ubuntu install before the change.

The day after changing my MOBO I was getting drive error and the PC would not boot. After messing with it for a good day I decided to reload Win 7 onto Disk1 figuring the issue was I changed the MOBO. Turns out it was an update I needed to do to the BIOS. So I was left with Disk0 - original win 7 install and Disk1 new win 7 install. I never until a few days ago had them both plugged in at the same time. I used to do a shut down and unplug and re plug. So both 100MB partitions are actually system partitions.

OK Ill try that and let you know how it goes. But some info I didn't mention which may be part of the issue or help my cause:
Disk 1 was my original Win7 install before changing my MOB and CPU.
Disk 0 was my original Ubuntu install before the change.

The day after changing my MOBO I was getting drive error and the PC would not boot. After messing with it for a good day I decided to reload Win 7 onto Disk1 figuring the issue was I changed the MOBO. Turns out it was an update I needed to do to the BIOS. So I was left with Disk0 - original win 7 install and Disk1 new win 7 install. I never until a few days ago had them both plugged in at the same time. I used to do a shut down and unplug and re plug. So both 100MB partitions are actually system partitions.

They may be labeled System Reserved but the System boot files are on DISK0 as evidenced by it being the only one with the System flag.

I'd be concerned about GRUB corruption if you didn't wipe the HD which held GRUB before installing Win7.

But work through the repairs as given to see if the problems clear up.

I don't think its GRUB because I never installed it when I was running Ubuntu and I did delete all partitions on the drive and formatted it before the 7 install. First a quick format then a thorough format. I'm going to try your idea above (unlpug and run repair) today and will let you know how it goes.