Issue with G4 MDD - on boot getting a "need to restart" message

I am hoping someone might have some insight on this issue. I have a G4 MDD dual boot, 1.25GHz, OS 10.4.11 and 10.5.8 (along with 9.2.2). I recently started the Mac up. It went through grey screen, blue screen and to my desktop. When I tried to open an app I immediately got a "You need to restart your computer" message. Tried restarting a couple of times as this has worked okay in the past. Not this time.

I next started in SUM so I could run Applejack. I ran Applejack in "AUTO" mode which does what is described as a "deep clean". All 5 steps went well with some minor repairs with the exception of one of the steps (I don't remember if it was the 3rd or 4th step). During this step it tried to access Disk4X10 - I do not remember the exact id. It took several tries before Applejack was able to do so, but was eventually able to complete the rest of the steps. I assumed the problem drive was an older SCSI drive that I only use for recovery purposes on rare occasions so I was not concerned. I exited AJ and restarted from my 10.4.11 HD. I got the same result with the restart message.

I next booted from my Drive Genius disc. I ran a repair on my boot drive and DG said it appeared okay. While I had DG running I decided to clone the boot drive to an external USB HD I have. I assumed since the boot drive icon was 1) showing up on the desktop, 2) I was able to get all the way to my desktop on startup and 3) DG could "see" the drive to run diagnostics - that I could clone the drive. The boot drive is a 75 MB and the cloning process took a little over 2 hours which seemed reasonable. I am also assuming I can reverse clone my boot drive from this clone to a new HD and everything "should" be back to normal. I realize that is assuming the cloning process had zero errors.

Since I had an older backup of my boot drive on another HD inside the Mac I tried to boot from it today. I got the same result as when I tried from the main boot drive. I also have 10.5 on 3rd internal drive and am able to boot from that without issue. When I looked at the 10.4 boot drive from that boot most everything is there - all apps and everything in the "Documents" folder - with the exception of when I look at the folders in myname where all but 3 show nothing in them. I backed up all of my most important stuff - financial stuff, etc. - on two different drives. These were in a folder I had named "Appleworks Documents". I cannot find this anywhere as of yet. I zapped the PRAM today and ran Disc Utilities, both verify and repair - which fixed several issues. I do not loose settings - clock etc. - so I am confident the battery is okay. I do not remember the last time I changed it, but it could be as long ago as 3 or 4 years.

My main question is why am I not seemingly able to move past the desktop when booting into 10.4.11? Is it due to the fact it's a "dual boot" machine? (I did do a "rebuild" with DG but it could not finish the job due to issues it found. (I'm assuming the dual boot thing is responsible.) What steps can I take to rectify the issue? Thanks for any help or insight anyone can offer.