setup/repair doesn't see my installed XP

i have...

20 gig HD: 2 partitions - C: Win98 D: XP Pro
40 gig HD 1 partition - G: XP Pro fresh install

just bought a new 7200 40 gig HD, so i stuck it
in as the secondary, installed XP Pro fine, and
i then got dual boot options for all three as
required. i wanted to install XP on the new drive
cos its obviously faster than my old one.

all was working fine until i had the not so clever
idea of moving a few cookies (within Win98) from
my old XP install to my new one. on booting up
from my latest XP install on G:, i now get

"system files corrupt or missing : system32/config/system"

ok, so i figured its a simple tale of repairing XP with the original CD, my PC set up to boot from CD and go through the repair motions.

on setup from the CD rom, it won't find my new
faulty XP install on G:, it just finds the old
working one on D: and offers to repair that.

new drive still seems to be working fine, and can
be read from within my other installed OS's.

any ideas?!

BACKUP
FORMAT
REINSTALL

Why do you need XP 2 times?
Use the working win98 to format the new drive, put all your data on the new drive and remove it. Format and reinstall the old drive with 98. Reconnect the new drive and install XP.
It always seems to work better when you start from scratch.

O, what the hell.
Have you tried to go back and remove the cookies you put in. More than likely Windows is seeing the "extra data" that it doen't have indexed as corrupted files. If nothing else just delete all the cookies from the directory (if you don't remember which ones they were)

Also, if you haven't installed very much software to the new XP install you could just rebuild it without fomatting.
In XP setup go past the repair option and continue with the clean setup and just have it delete the files in the windows directory when it finds it, and reinstall XP and whatever software you had installed.

cheers Rifleman for replying. in the end i just formatted the new HD and installed XP again.

the reason for having two XP's? well, after about a week or so, i will delete my old XP install once i get the new one up and running the way i want it.

Format and clean install is always the best bet. There are ways of repairing all the files, but it is very time consuming, and very hard on the hairline. Plus it just never works as good as a clean install.