First, thank you for helping me with this.
OldsmobileMike has already been helping me a ton with some private messages with advice, but I don't want to abuse his time either!
My System:
A3000 Super Buster 11. GAL chips recently replaced fixed garbled graphics.
Battery has been replaced with coin cell upgrade.
3.1 Roms
OS 3.1 Installed
Warpengine 3040 with 32 megs of Ram installed.
2 megs of chip. No zip ram on motherboard.
750 Meg Scsi hard drive attached to Warpdrive.device (the warpengine fast scsi II).
External Lacie CDROM Scsi attached externally to scsi.device (a3000 onboard scsi).
Currently I don't own a working internal floppy drive so I have an external Amiga floppy drive plugged into the external floppy port (DF2 on my system. works good)
PicassoIV graphics card.
AD516 Sound card
Personal Animation Recorder with IDE hard drive attached.
The Goal: 3.9 installation with all the boing bags successfully installed!
The Method: I was planning on following OldsmobileMike's awesome videos on doing this install but I have already run into some hickups.
What I did:
1) I inserted the 3.9 CD and first thing attempted to make a emergency install disk. Program returned successful creation message.
2) I try to boot with the emergency disk and I get a crash saying something about "setpatch" and string of numbers 00012020021 or something.
3) I make a backup of my entire Workbench partition to a folder on my Work partition.
4) I boot from the install disk of 3.1 and format the workbench partition.
5) I do a fresh install of of 3.1
6) I mount 3.1's CD0 with my appropriate scsi drive and unit number.
7) I insert the 3.9 install disk and run the installation "upgrade from 3.1 or blank partition". When it finishes, I install the internet software from the CD as well.

I reboot and insert a CD I have burned from my PC with the latest Picasso96 software as well as the Boingbag1, boingbag2, and boingbag3/4 combo. First thing I notice is that the files names on the CD are all truncated to names like boing~1. I was hoping the 3.9 install was going to fix this filename shortening issue but apparently not.
*** I also notice at this reboot that Amidock is crashing on reboot and not loading, but I click suspend instead of reboot and I can still access the system***
9) I attempt to unarc the picasso drivers and I get errors for some of the files as corrupt. If I click past the error messages most of it decompresses fine but some of it definitely had a problem.
10) worried about this corruption above, I opt to use my original picasso96 install disk and install the software so I can run a larger RTG screen mode. The software seems to install fine and I am on a larger screen mode. Amidock is still crashing.
11) I attempt to unarc the first boingbag 1 archive which of course is listed as boing~1 or something shortened like that. I run into the same issue getting system messages of some of the files being corrupted. Pressing "ok" through the process what I am left with is enough to launch the boingbag1 installer but it asks me for the 3.9 cd to be inserted and as soon as I insert it the installer crashes and says there is something wrong with my install files (I'm sure its the corrupted files).
So, now I am not sure what to do. I can't install 3.9 on a freshly formatted partition because the disk fails to make an emergency install disk crashing on setpatch. Installing over a fresh 3.1 doesn't seem to be a good option either as I have amidock crashing right out the gate. My CD Rom has been working flawlessly in the past when installing Amiga software (like photogenics for instance... I installed that last week and got no errors), but CD's that I burn on the PC with amiga files I need seem to all get their names messed up and files seem to be corrupted on all the archives I burn. Not sure if this is related to the filename issue, or something else entirely. I apologize for typing so much but I wanted to give as much information as possible.
Thank you again for any help you can offer to help me get through this OS upgrade.
-Dan