I think this fits here better then the MS tuning pages as I don't *think* this is a tune issue, but open to ideas as I've exhausted all of mine.
Friends car had been running great. Drove it into the garage after a trackday, no issues. Tried to start it a week later and it only runs on two cylinders(2 and 4 dead). Full sync while running, no sync losses, just runs like a tractor on two cylinders with frequent pops out the exhaust.
At a complete loss, asking for any ideas no matter how spitballed or out from left field they are as I emptied my bag of tricks inside a few hours.
Car is a '00 chassis with a BP4W on an MS3, LS coils(still wired in Miata fashion for batch fire, 1-4, 2-3 using OEM wiring), stock injectors/pump.
Tried:
Swapping coils(Runs on LS coils so easy to change)
New plugs
New crank sensor(just so I could say I tried it)
Test mode shows good spark on all four, and the injectors all go click click click when tested.
The major grounds at the rear of the PPF, top of the intake, and engine to chassis shelf are all clean and good.
When car starts it needs throttle held open to run, and the spark wires for #2 and #4 can be pulled with no effect on RPM, so I know those cylinders aren't firing for some reason. I'm thinking its fuel related as we have changed everything spark related, but at a loss as to what would cause two injectors to not fire during engine running, but be fine in test mode.
Log/tune attached for any help they might be.

 

Have a timing light? I use them to check if there is spark at each cyl. I doubt it's spark after you changed those things (and the fact it's 2 and 4) but it's a quick, easy test.

 

I pulled each spark plug out and tested them with the MS test mode... Each one showed solid spark from 500-6000RPM. I guess I can try with the timing light just to see if they are firing under load...
Yesterday I also pulled the top of the manifold and replaced #2 and #4 injectors with spares... No change. Tore down the front of the motor and verified timing hadn't slipped(it hadn't) and compression checked each cylender(210 across the board, it's a 12:1 motor with a head shave).
At this point I'm honestly looking for a spare 99-00 MS to rule out something internally wrong with the MS3 that's currently installed, even though it's less then 2 months old. I feel like I've checked and double checked everything mechanically with the motor and wiring. I have spark, I have fuel, I have compression, I have RPM sync. Untill I turn the key and then I apparently loose something from those two cylenders.

 

Yeah, I like to check spark under running conditions.

After that, any chance you have an O scope or similar to check that the injectors are getting a signal to fire while running?

 

I just had a quick look through the ignition settings in the tune and compared them to mine (2000 with DIY LS coils running "stock" batch ignition). My settings on the left, yours on the right. Differences Highlighted.

What's causing the issue is (almost certainly) the "Number of Coils" setting. Mine is set to wasted spark, yours to Coil on plug (Sequential). There are a few other differences between the two, but I think that is the one causing you grief.

 

Muffins, your the man. I have absolutely no idea how that changed... its not exactly something you can "accidently" change as it requires a power cycle to take effect. I didn't even think to look there as I hadn't considered it a possibility.
Changed that to wasted spark and it fired right up. Thanks so much for taking the time to dig though those settings!