If you can get it to run in windows now can you not try a restore to an earlier date ?
If not :
Using the boot disk, let it boot into dos by selecting Start PC without CD rom support and at at the A prompt type format C: /s
Press Y and then hit the enter key when warned that this will delete all information on this drive.
This will take a little time and will wipe everything off the drive assuming that it only has the C partition.
Reboot with the boot disc in again and select the option without CD rom support again.
Place the ME cd in the cd drive and this time at the A prompt type E:\setup
This is where the cd drive would normally be D as it moves the letters up one as it creates a virtual drive D to temporarily store the files needed to run dos.
If you have more hard drives/partitions then the letter in place of E will be one higher than what your cd drive normally is.
Then just let it do its stuff and put your serial number and details in as it asks for them