Following up on the problem for future reference...
I'm not positive why this worked, but here is how I got it running again.
I tried another A4000D (like it was last used in) and it caused a very similar problem so it wasn't completely 4000D/40000T specific.
This one did boot with the RES jumper set, so I installed the Deneb software from it. It's hard to clean reinstall an Amiga without a PC with a floppy drive or an Amiga with USB or CD access, so I used the built-in, not updated version.
I rebooted with the ROM jumper set to disable the ROM.
I tried clearing the ROM, but it was already empty. Instead I loaded the Quickstart configuration and flashed that into it.
After powering down and changing the jumper to normal, the system booted and worked.
I haven't tried it again in the 4000T, but for now I'm planning to use the 4000D anyway.
Maybe this will help someone. If I do use it in the 4000T in the future I'll update this thread, but I've been meaning to buy a second and third Deneb anyway.