T61 - Did using the SATA bay somehow corrupt my XP install?

Detailed explanation follows, but the executive summary version:
Can't boot from the HDD in the machine if the CD bay is inserted. With the SATA ultrabay installed instead, I can only get a normal boot from the SATA bay HDD, not the normal drive. Are there are any known issues using 2 bootable XP HDDs in the machine and in the ultrabay at the same time?

I bought a new Hitachi HDD, installed it in the TP61 and have spent lots of time tweaking, configuring, removing and installing apps. Was almost ready to do a backup (of course!) and remembered some downloaded file data I wanted on my previous Seagate drive. I swapped out the CD ultrabay and booted from the old Seagate in the SATA ultrabay, copied the data to the new Hitachi and rebooted which I had done before in this process...BUT, this time I forgot to reinsert the CD ultrabay before rebooting so the TP61 booted from the Hitachi with the Seagate present in the Ultrabay. It booted with a partial desktop but appeared to hang on installing drivers for the new "found" hardware which I think was the ultrabay.

I finally got the machine shut down, replaced the CD bay, but the Hitachi would not boot just getting the blue boot screen, play the Win login sound, then play the win shutdown sound and just loops through playing this login/logoff sounds process (I had autologin set via tweakXP) until I power it off. Found web references to login/logoff boot loops but no solution worked. A retail XP CD booting from the ultrabay with repair option can not find a hard drive. It won't boot into safemode. If I reinstall the SATA HDD bay again and select it to boot from, it boots fine from it and can see the Hitachi drive. Rebooting with the Hitachi again selected as the boot device will now boot if the Seagate is present, but it seems to get a "mix" of the XP installed on the Seagate and the XP installed on the Hitachi

Each machine is partitioned with a primary for the OS, and extensions for the apps and the data i.e. C, D, & E along with the hidden recovery partition. When I boot with the Hitachi I see the desktop as configured for the Hitachi, but the C boot drive is really from the Seagate. Using diskmgmt, I see Seagate is disk0 with C, G and H drives while the Hitachi is disk1 as the D, E, and F drives.

Whew, did that makes sense? Short of reinstalling from scratch again, is there a way to get the installed Hitachi HDD back as the C, D, and E drives? Is it completely toast or is their some boot/configuration setting that could be tweaked to make things good again? Perhaps a registry entry that got hosed? I'm out of ideas. Thanks much