Megasquirt 2 and 3 have a very handy test mode that allows you to test outputs to help determine faults and validate functionality.
CAUTION!!! USE AT YOUR OWN RISK
Turning certain outputs on can be dangerous and it is possible to overheat your ignition modules or flood your engine by turning on the wrong outputs. So be careful whenver activating an output!
The main outputs to avoid turning on are injector outputs in use and any spark outputs in use. For ms3 this will usually be Inj A to Inj x and Spk A to Spk x (x being the amount of outputs in use). For ms2 it is usually the spark outputs LED15 and LED16 as well as the injector outputs 1 and 2.
The test mode menus can be found under “CAN-bus/Testmodes”.
The Output test mode menus allow you to turn ON/OFF any of your outputs or pulse them at a certain frequency and duty cycle. For example if you have just installed a boost solenoid and want to check if it is working you can pulse the valve at a certain frequency and listen to see if it is actually pulsing.
There is also a separate test mode for injection and spark. This test mode menu allows you to pulse your ignition coils as well as your injectors.
Coil Testing
Output interval(ms) – sets the RPM the coils will be tested at
Coil Test Mode – Test one coil at a time or a sequence of coils
Coil Output to Test – Which coil to test. If in sequence mode it will fire the coils in sequence until it gets to the chosen coil
Dwell – sets the charge time of the coils for the test
When testing ignition coils it is a good idea to insert a spare spark plug into the coil and rest it on the valve cover or something else that is grounded and be careful to keep your hands clear during testing or risk a nasty shock.
Injector Testing
Same settings as above but pulsewidth(ms) and the number of injection events is chosen. 
Bartune Engineering 