I read the 30 pages of the post to get a feeling of what the project has been through.
It is incredible, you put a lot of effort in this. I enjoyed a lot reading this.
Seems this 7010 is a good candidate, it has 2,1 MB of block RAM, VRAM and the 68k RAM can be implemented in it. (the only thing I miss from the Cyclone III, some more BRAM). Maybe you could port the MiSTer version, it also uses BRAM for VRAM and 68k RAM, and DDR3 SDRAM for the ROM.
It was my preliminary idea to port the MISTer version as I consider the Cyclone V and Zynq more or less the "same alternative" but from a different vendor.
This Zynq version is a little bit low in BRAM, I think the 7020 would be more resource comparable to Cyclone. Anyway, I think it is enough for the task.
There are other cores, which should benefit from some care.
If I can make my board work, I think I will try something with Arcade cores. Maybe most (or all) Mega Tech - Mega Play boards are now very easy to recreate with all the work all you did with this core.