MBR issues - Don't do this unless you know what you are doing!!!

Drive letters in WinPe will probably be different from what you see in windows - that is normal.

I would delete the bcd store and run the commands again. Yes you should be pointing them at the reserved system partition .

Otherwise, at cmd prompt, type:

diskpart

lis vol

( Look to see the drive letter for your main windows partition - if it is D then type as below, otherwise replace D with the letter diskpart gives for the main windows partition)

sel vol d

act

exi

bcdboot d:\windows /s d:

bootsect /nt60 all /mbr

restart the pc - you're good.