The prior suggestion shows some merit; however, ALL Hard Drives take Drive letters before the CD-Rom. You may not set the CD-Rom back to E:.
Unfortunately, you are left with a few choices. You can open the registry and do a search for anything pointing to e: and swithc it to F: AND modify any of those config/ini files. Most of the applications now reference the CD-Rom from the registry information. For example, Look under HDKey_Hardware/software/microsoft/windows/currentversion/setup/. You will see a line that tells you where your source files came from (Most likely the CD-Rom or windows\option\...).
Note: You will also run into this problem if you modify your partition count. That is if you make you 8.4G HD in to 2 partiotionsinstead of 1. They will give you C: and E:, assuming you have an additional HD (D:).
I generally push my CD-Rom Drive letter out with a fresh build. Set the CD-Rom to M: so I never have to worry about moving them arround.
BTW, PowerQuest Partition Magic includes a Magic Mover program. It is designed to handle this exact problem (more related to partitioning drives). It is an exceptional piece of software. It allows you to change you partitions from fat32 to fat16 to NTFS, plus many more variants with cluster sizes. Best of all, it converts you data. I have never lost a file yet using it. (Though I should backup much more often than I do ;)
I hope this helps you out of your bind. BTW before you mess with the registry make sure you back them up first.