Looking through the FAQ, I may have a problem. To get the MMR working, it runs a config program in the startup-sequence. So, if I don't have that going, the machine is just an A500 with 8MB of RAM instead of the 68030 with 12MB RAM. That may be a problem.
Add the program into the startup-sequence of your 3.9 ERD disk, or whatever it is you're booting from to install 3.9. Then copy it into the same location after the 3.9 installer completes (I assume somewhere obvious, like the first line of your Startup-Sequence).
Should be fine, my A500 does a double reboot each time I fire it up, as well. Once to add the 32-bit memory on my VXL*30, then again to load all the 3.9 LoadModule and LoadResident replacement libraries. I swear one of these days I'll get around to learning how to burn my own custom ROM's! :lol: