Update. After almost a week of messing with it, I got everything working. BLUF: the only thing that has made sense is that there is a problem with my Raspberri Pi.
I started by using bossa and reflashing the duet 3... that didn't fix the problem.
I remembered I had a few Raspberri Pi 3 laying around from other projects as well as I had purchased another duet 3 for my other printer. I decided to swap out one thing at a time, starting with a new SD card.
I then used the new SD card and started with a fresh Duet Pi image. I was still getting errors/incompatble firmware and Error: M997: Failed to find IAP file /opt/dsf/sd/sys/Duet3_SBCiap_MB6HC.bin
I went back to follow the https://duet3d.dozuki.com/Wiki/Getting_Started_With_Duet_3#Section_Updating_Duet_3_from_RRF3_0_Beta_12_to_3_0_Final_via_DWC
After following that Wiki, it got rid of the incompaable firmware but still said it was missing the Duet3_SBCiap_MB6HC.bin
I then changed only the Raspberri Pi keeping the same SD card and Duet, and after the sudo updates/upgrades everything was working.
After that I was done with that duet 3 and SBC setup I decided to setup my other new duet 3 and duplicate what I did as both setups are going into 2 identical printers.
Well to my surprise, using the Pi3 that I was using on the first setup, I started having the exact same issue on the new duet 3. I then grabbed my last Pi 3 I had and swapped only it and everything worked on that setup.
So, with all of that I can only conclude that there is something wrong with the original Pi3 I was using however, I do not know what.
I know not everyone will have extra Duet 3's or SBC's laying around, but this happen to be the fix for me.