I would not have suggested removing the drive letter from System Reserved if it could cause problems. We have worked through these issues here since long before Windows 7 was released.
I'm also aware that better performance can sometimes be had by moving the paging file to another HD, but my suggestion is to try it System Managed only to see if it affects your perfomance problems.
You might wipe the boot sector with Diskpart Clean Command
from the installer command line before reimaging again to see if boot sector corruption is involved: DISKPART At PC Startup