Slow Starting up

Could this cause the slow boot I mentioned earlier?
I had a stable system but got fully locked up while trying to perform a
Ghost backup. Before formatting my C drive and do a fresh install, I
installed XPSP2 on an empty partition of another physical drive (E: on
disk2). So I could inspect my C drive and save some data. After this I
formatted C and did a fresh XPSP2 install on that C drive. What I think I
did wrong was to just delete the OS files on my E drive, because I didn't
need them anymore. Did I confuse the boot record on that disk, resulting in
a long search before I can op "My Computer"? Thanks for any advise.