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new 99 dollar 500mhz 68020?

Hmm, I don't remember the details of that now, but for most purposes I don't think it's essential to get an exact clock speed match for the original hardware, as long as it's pretty close. Yeah, those internal clock dividers are somewhat limited as to what frequencies they can do, so if you really need exactly 15.6672 MHz or whatever, you'll need to use an external oscillator to get it. What's more important than the exact clock speed is the relative speed of the various clocks, as you said. If all the clocks are ultimately derived from the same master clock, then you shouldn't have issues with edge synchronization.

It's been a few years since I looked at it, but I think one of the problems with Plus Too was that it was pushing the flash ROM to the edge of its timing specs, and I didn't understand the synthesis software well enough to set up proper timing constraints for the ROM access. I suspect it was occasionally fetching a bad value from ROM, causing the instability problems I observed. I never really figured out a good way to debug problems like that - I could debug functional problems like a reasoning error in the design, but not timing or electrical problems.

 
So you were using an external Flash ROM? The newer Xilinx FPGAs have Block RAM slices that could be used as the ROM storage, and it wouldn't be terribly difficult to load the Mac ROM into BRAMs from the bitstream. Such a setup would not have any of those timing issues.

 
I notice that the Minimig (Amiga) AGA on MiST is running a 68020 - and the TG68 core is posting 100MHz+ speeds.

 
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Though I'm not quite sure I'm following this correctly, this person seems to be running an FPGA-built 7MHz 68000 Amiga with a 28MHz TG68 core.  (Found via the MiST github wiki)

 
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