More things to note:
1) I also have KS 3.1 ROMs installed.

2) I simplified things a little by only including the PAL and NTSC monitor drivers. I originally had a lot more in there.
3) The system does not GURU when I boot with my ACA 1232 accelerator removed. However, I just see a black screen and no other activity.
4) I can boot from my WB 3.1 floppy and see the System partition on other desktop icons from the OS 3.9 install and access the data on the CF just fine.
5) My ClassicWB 3.1 (LITE) system I installed on a 4GB CF for my A500 boots fine in the A1200 with or without the accelerator.
Seems like there is something about the installed OS 3.9 the real Amiga 1200 does not like. Maybe I will try putting a plain vanilla OS 3.9 w/BB2 on another CF see how it likes that.
I wonder if I need to be using ACATune? The A500/OS 3.1 system did not need it but then it was being used with an ACA500 which did its own thing with Kickstarts.