Just an update, my hardware came in on Wednesday, and as of last night, I have a working Megatouch XL, running Titanium. You'd think after years of tearing things apart, I would have learned to take pictures of wiring routing, and connections before I disassembled things, but I guess I enjoy the pain...
There was no jumper on the HDD when it arrived, so, it took some trial and error to get it working. Just in case anyone else has issues in the future, here is what happened with all 5 jumper settings on my HDD.
CS (closest to the Molex) - Drive recognized in BIOS, the system would boot up as far as initializing the touch screen. Then I would get a message in pink text stating "Hard drive copy error"
Slave - Recognized in BIOS, but gave me "Bad command or file name"
Master - Not recognized in BIOS, and gave me the insert system disc message
Blank - same results as Master
PM2 - WORKING MEGATOUCH!!!!!!!!!
Now, from what I'm reading about the PM2 setting, it looks like it may be indicative of a pending drive failure, but I guess time will tell.
So, back to my original issue. I changed the jumper setting over on the I/O board, and swapped out the HDD for the CD-ROM, and tried to run the CD that came with my machine. I'm still getting the boot disc error. I was successful in making an ISO of the CD with IMGburn, so from what I read, that means my CD is ok. Do you guys have any ideas?