Well, I have made some progress but not in the expected way.
I have never been able to make a proper, working emergency-disk. I didn't write down exactly all of the problems but I had random issues making the disk but if I did get one made it seemed to be either incomplete or for some reason always failed for one reason or the other.
Maybe the version of the 68040.lib or scsi.device had something to do with it.
I ended up installing 3.9 and BB1 and BB2 thru WinUAE, made a LHA archive of the result using Filemaster3 on my Amiga911.adf thru WinUAE and then used the same when transfering back to my real Amiga 3000. Result, this time it booted with no crashes or system requesters showing and 'about' showed OS3.9 correctly whereas before even after 3.9 install, 'about' still showed OS3.1.
When I had previously installed OS3.9 thru WinUAE without the BoingBags, the install would never work when transfered to my real A3000 not matter what I tried.
Something in the BoingBags must have fixed the issue. Sadly, if it wasn't for WinUAE I would have never been able to get this far..... Very difficult process to say the least... at least for a novice like me.

THANK YOU EVERYONE FOR THE HELP, as you could tell I was beyond frustrated for which I apologize.
