i can't really add anything helpful apart from that i was in the same situation figuring out how to get the CV64/3D's A4000 scandoubler into the ECS video slot.
i figured that i (was too chicken) didn't want to butcher the slot or the card so just plopped in an indivisionECS and bolted the extra VGA out to the CV64/3D's backplate.
i was worried that there may have been other signals like sync-on-green that the A4000 had that the A3000 just didn't produce, that the SD/FF looked for to generate a stable signal clock.
good luck with what you're doing though, you're a braver soul than me - i just hope you don't cook anything!
