You should be able to configure a button on a controller to bring up the menu in MiSTer - I know I have that ability at least. I can't remember the last time I had to have a keyboard plugged into mine (probably just at the initial setup).
Hmm, if I adjust the 'knob' on my replacement board, it now affects my New Astro City (it didn't with the old board).
It makes it too bright and washed out. The Scart out seems to be fine, just the JAMMA video signal to the cab.