I freshly installed a new MegaSquirt into a 1994 M Edition Miata and after fiddling with setting and trying to start it up only two cylinders are firing. At first I thought it was just crazy rich but when I pulled the plugs, plug 2 and 3 were soaking wet and 1 and 4 were fine. I followed DiyAutoTune's install instructions, and used the base map available at megasquirtpnp.com. Uploading the msq files to MS get the errors:

15 Warnings:
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:IdleCtl equal to the proposed PWM Warmup
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:can_poll equal to the proposed Disabled
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:rtbaroport equal to the proposed SPAREADC
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:ego2port equal to the proposed SPAREADC
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:flexport equal to the proposed PA0
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:boost_ctl_pins equal to the proposed PA0
Warning: baroCorrVals array size does not match the currently loaded configuration,
rescaled .msq values to match configuration.
Warning: baroCorrDelta array size does not match the currently loaded configuration,
rescaled .msq values to match configuration.
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:launch_opt_pins equal to the proposed FLEX
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:N2Oopt_pins equal to the proposed Flex
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:N2Oopt_pins2 equal to the proposed PT7+6
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:testop_coil equal to the proposed CoilA
Warning: Parameter in .msq, but not valid for current firmware: No options found for Bit EcuParameter:testop_inj equal to the proposed Neither
Warning: idleadvance_curve array size does not match the currently loaded configuration,
rescaled .msq values to match configuration.
Warning: idleadvance_loads array size does not match the currently loaded configuration,
rescaled .msq values to match configuration.
Testing the coils in tunerstudio I can get spark from a few and when I test coil d, the fan relay clicks and the fan turns on. Straight witchcraft. Installed stock ecu back in to check if the coil pack was damaged when I installed megasquirt but it started and idled fine. I have tried changing all the basic required settings to get it to run to no avial. Is this an issue with wiring, issue on my part, or a software problem? This is my first time doing any kind of tuning and I am probably in over my head. I am more mechanically inclined than things with software and electronics. Is this something that I am missing or could the map not be compatable with the version of mega squirt I am on? Any help is appreciated!
Specs:
Stock AFM
Stock 1.8 Injectors
Innovate Mtx-L Wideband
MSPNP2

 

Upload your .msq file

 

2017-02-08_16.48.33.msq This one?

 

Nothing blatantly off about that tune. Can you try using output test mode to see if any injectors or spark outputs don't fire there?

 

Using the output test mode, Coil A fires cylinder 1 and 3 / Coil B fires 2 and 4. Coil C does nothing and Coil D clicks the fan relay and turns the fan on. Individually testing the injectors, each one fires fine. Are all of the warning ok when I load the tune?

 

Sounds like you've just got the ignition leads around the wrong way then. Spark A should fire cylinders 1 and 4 and Spark B should fire 2 and 3.

 

Leads switched so Coil A fires 1/4 and Coil B is now 2/3. Still having the same problem, running really rough, stumbling idle. Sounds like a misfire, checked plugs again, all black and soaking wet, before they were just scorched. Afr is reading 7.5, as low as it will go. Too much fuel now? Also there is a humming from the front but from what I have read that is the pwm valve?

 

Can you post a data log of the problems running now that the spark plug wires have been fixed?

 

2016-10-14_10.16.05.msl
Had to give a little bit of gas to keep the engine from stalling out

 

If the wideband is calibrated correctly and has actually warmed up and started operating in that log then you're way too rich.