Ok first things first. Whenever your playing with Linux and Windows please have a Win 98 startup disk. It's the best thing Bill Gates ever made.
If your computer is still picking up the 2nd HDD disable it from BIOS. Then the computer can't see the HDD at all. That should fix that problem if it's still see'ing the 2nd HDD.
Ok here is why you want the Win 98 startup disk. Boot from the disk. No need for CD-ROM support apon boot. When your at a DOS prompt type 'fdisk /mbr' this will clean your mast boot record and then it should all work fine.