The CD rom is connected to secondary IDE on the motherboard while the HDD is on primary. I'm not sure how much o f a difference it would make
Definitely the CD-ROM should still be detected if you used it to install Win9x, since it's on the secondary (even on tertiary and quaternary controllers, so long as they're on the right port and interrupts). It won't, however, if you've got the (!) on your hard disk controllers or often if they're just showing up as a "standard" IDE controller.
Renaming the CONFIG.SYS and AUTOEXEC.BAT (I reverse extensions for non-palindromes, and invert the palindrome extensions, so .BAT becomes .TAB, .COM becomes .MOC; .INI becomes .NIN, .SYS becomes .YSY and so on) will eliminate DOS drivers as being the problem.
I'm also loath to use "cable select", rather I jumper the drives to match their intended status and make sure I put them on their correct spot on the cable, but probably that's not too huge a concern if a DOS driver detects the drive.
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