[Solved partially] Legacy Same Drive Dual Boot Broke

[el lissitzky]

Update: Despite 99% of the research I did suggesting the cause was a corrupt boot sector/MBR, the issue appears to be isolated to my Clover boot loader because upon attempting to boot with a Chimera USB Win 7 booted perfectly fine.

 

Background: I have a machine that was previously dual booting legacy El Capitan and Windows 7 off of the same drive on a non-UEFI board.

 

Issue: When I try to boot the Win 7 entry through Clover I get a "Disk Read Error".

 

Possible causes: The El Capitan install is a recent fresh replacement of the Mavericks install. I will try to retrace my steps that may have caused this but the troubleshooting took place about a month ago and was a lengthy process. 

 

1. If I recall correctly, upon first installing the new El Capitan, Clover was not loading off the drive and instead I was getting a Windows boot menu. To remedy this I think I had to switch the Boot0 to AF or SS. After that I can say with certainty the system was booting both OSs fine. 

 

2. Then there was an issue at some point where the EFI was improperly formatted as HFSJ so I had to set it back to FAT32 and I think at this point the dual booting was still in tact.

 

3. At a later point I tried to format the EFI again in order to troubleshoot another issue but accidentally improperly formatted it. In order to fix that I found a post on Stack Exchange that detailed out to swap the EFI out from starting to ending byte with the EFI from my boot USB.

 

4. I reset my BIOS to factory defaults.

 

These are the possible things that may have caused this issue but I'm not sure.

 

Questions: 

 

• Is my boot partition damaged?

• Is there BIOS or Clover setting causing this issue?

• Is there a possible way to examine the boot partition or see a detailed log that may hint at what is causing the "Disk Read Error"?

• Is there any possible way I can repair this with out having to install both OSs from scratch?