Integrity checks would not finished successfully. I went with a full on repair which didn't want to run the last few times I attempted it due to Jet Errors -501, I'm thinking that the CHKDSK which moved a few thing around may have fixed that. Note: I did run SFC /SCANNOW and no issues found. When doing an integrity check on the NTDS.dit it stated that the file had not been shut down properly or cleanly, so some data was basically not synced in comparison to some of the log files.
ESENTUTL /p C:\Windows\NTDS\NTDS.dit
Did a Lossy repair on the Active Directory Database file. Made sure to make a backup of the entire NTDS folder before doing anything.
Then make sure to rename the edb.log file to something else such as edb.log.bak.
Restart server normally, cross your fingers and hope for the best. Worked for me
2 days worth of fighting with this thing and some long nights, so happy to be done with it.
Thanks for the input JBI and Ryu, much appreciated one way or another. Yeah I didn't realize JET errors are MS Access as I have little to no experience with Access. Funny, I guess they had to find some way to reuse Access which seems like a dead product, its old from what I can tell, makes me think of FoxPro (Still have a customer running ancient software on FP6).