Compression test : just unplug Megasquirt?
 

Thinking this through here...if I unplug MS that kills the fuel pump and ignition, right? so then just crank the engine while holding down the throttle to get my readings with all plugs removed, correct? thanks!

that would work.

personally i just unplug the CAS, but i'm not sure how accessible that is on a miata. with no RPM signal you get no spark, fuel, etc.

No need to unplug the MS, just unplug the coils and hold the throttle fully open, the MS goes into flood clear mode specially if you have a TPS set up for that.