Can you show us what in the registry now?
regedit
Select HKEY_LOCAL_MACHINE
File - Load Hive...
E:\Windows\System32\Config\SYSTEM
SYS
Select HKEY_LOCAL_MACHINE\SYS\ControlSet001
Your partitions are not GPT so UEFI boot is not an option at this point. I will try on my system if it will work but in the mean time let's recreate your BCD.
attrib -s -h c:\boot\bcd
ren C:\Boot\BCD BCD.sav
bcdboot E:\Windows /s C:
Reboot