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Reviewing the FSM COMBEL pin out description for the 500khz clock, and 500khzW clock, the pin number are assigned the same. This is not the case. Removing the ACIA from its socket, lifting and tying pin 4 to 3 where the external 500khz clock is attached solved the boot issue using the cartridge port.
This is also somewhat explained in the Nemesis installation manual.
The machine will boot the cart with a 50mhz main clock with keyboard function.
All else is normal.
This allows me to test various changes to hardware, and at least have a limited set of diagnostic tools.
Next test will be with an Eagle Sonic installed to test 50mhz CPU/ 25mhz bus.
No software will be harmed, the 50mhz input to the Eagle Sonic will be directly feed. This is already known to work on this machine using software selection booting TOS, however never addressed the kb failure while using the diagnostic cart.
Then move onto reinstalling the AB040 and work towards stability at 50mhz, where I left off 20 years ago.
Thank you for your input, it was noted.