Repair Windows ME

I have an old Compaq 1200 laptop that was given to me with a 6gig drive
running Windows ME. The os got corrupted ( will only get as far as the
splash screen). I booted with the floppy emergency disk and ran scandisk. It
found several problems including crosslinked files. After many attempts(I
had to keep deleting documents to make room for the rewritten files scandisk
was making) I finally got a clean bill of health although my C: is full of
..chk files. They must be resurected files having to do with the damaged and
crosslinked files scandisk found. It did also find some files with long name
violations that it could not fix. It said that I needed to run scandisk from
windows to fix that. Well I still can't boot windows. I also don't have the
rescue CD and don't want to wipe the C: partition because I don't have cd's
for all the programs on it.

I do have the entire set of setup files on the D: drive partition. My
problem is, I don't know how to get those files to install. I type
"setup.exe" at the Drompt and it starts the install process but stops
because it says my C: already has a system on it and halts the process.

Also, scandisk put all sorts of directories on the C: (DIR00001) etc. Am I
to assume that the files in these directories are the bad files that
scandisk found or are they the supposedly "fixed" files?

How do I get the system to reinstall without starting from scratch? There
must be a way.

Any help much appreciated.