Here is my BOOT SECTOR (MBR) on disk 0 :I found some stuff about $Boot. If it is accurate and you are using a hex editor, it mentions it is 426 bytes with an offset of 0x54 and contains bootstrap code.
The MFT mirror start you mention is also 2 on both of my systems. One with only the one partition for Windows 7 and one a UEFI install for Windows 8. I was checking c: on both systems, but on Windows 8, C: is not the bootable one.
Do you believe the info about the boot sector number being different from the actual partition size is a factor? I am not familiar with something to change just that number, but I believe something like the bootable home version of Partition Wizard can rewrite/repair the records for partitions.
It all looks fine to me? On the web are layouts for it.
Used PM as suggested, CHKDSK of the partition finds the same problem.
I think the rebuild just runs the same commands I used before.
The number being higher than the end of the physical disk sectors could be causing the problem as CHKDSK tries to check stuff? Also the $MTF and other metafiles are at the end of the disk. There is probably a field somewhere, maybe in the boot record that defines the start of the partition and length or the partition end? See https://en.wikipedia.org/wiki/Master_boot_record