Can incorrect TS settings cause misfire?
 

MS noob here. I've been pulling my hair out chasing a misfire (that I suspect is causing my wide band to reading full lean no matter what even with changing the VE table up and down almost to the point of stalling) for a few days now and I was wondering if my TS settings are incorrect. Inside the Inj/Spark disable test mode disabling coils 2 and 4 will result in no change while the motor is running and disabling 1 and 3 will cause it to stumble. Swapped the coils around and still nothing when disabling 2 and 4 so is a result of the COPs being wasted spark? I disabled the injectors one at a time and each one causes the engine to stumble as well so I think they're all working alright. I set up base timing with the #1 cylinder and noticed I had to attach the inductor with the arrow pointing the wrong way but I'm not sure that's relevant. No exhaust leaks that I could find with soapy water. I did order new ignition wires but they won't be here for a few days so I'm just killing time seeing if anyone could look over my tune. Lemme know if ya'll need anything else. I'm running on a few hours of sleep so I'm a bit scattered brained today.

Mostly Relevant Specs:
Freshly built 2002 VVT
Stock COPs
BK7REs gapped to 0.03
DW 700CC injectors
DW 255LPH FP
AEM 30-4110
Stock fuel rail
Kraken full 3'' exhaust that has the O2 bung just in front of the shifter hole @ a 12 O'clock position
MS3 Pro PnP 1.5.1
MAP line feeding off the back of the intake
TS 3.1.08

A bad wideband O2 sensor will report lean on most controllers as this is considered a fail safer state.

Better check that out then. Is the brake cleaner test a good way to test it? It'll be annoying if my new wideband turned out to be bad.

If your wideband is reading full lean no matter what you give as far as throttle input or VE input, it's pretty safe to assume it's bad. Brake clean test will just do the same thing as forcing the VEs rich.

I also run an AEM 30-4110 and it came with a bad sensor that did the same thing. Pretty sure someone bought it, swapped the supplied O2 sensor with a failed one, and sent it back. Last time I buy fancy car parts from Amazon...

Side note, you can rule out your AEM controller by unplugging the sensor with the controller on. The reading should default to 14.7 with no sensor connected.

Under what conditions does the misfire occur?

The entire time the engine is running. Also you guys guessed it. O2 sensor is bad.

Right on. Yeah it sounded like it. Do you have a replacement on the way? You'll want to get that sorted and get your VE table/AFRs back to acceptable before proceeding or you might end up chasing your tail.

I don't have my computer with TS so I can't see your tune currently. Was the car running fine with the current tune and then the misfire occurred? Or has it always ran rough with this tune?

This part of the issue you're stating is curious. If you don't notice any running difference with ignition to cylinders 2 and 4 disabled, but the engine still runs with coils 1 and 3 disabled, that means you still have some level of spark reaching coils 2 and 4. If the issue is the same with coils swapped, you may have high resistance in the plug wires, or a partial open/short on the wiring going to coil 2/4.

If the misfire just began occurring with no changes to your current tune, I'd also run a compression test on the engine. It's a partial shot in the dark but also one of the only other tests you can perform until you get your O2 sensor in and VEs/AFRs back within spec.

I'm working on getting a replacement since the wideband was brand new. Just built the motor so basically it was misfiring right off bat but did start up within a few cranks first try surprisingly. I mostly used the base tunes from trubokitty with a few tweaks. Engine sounds like it will die with 1 or 3 disabled but I didn't toggle them off long enough to find out. I got the new plug wires in today and they didn't make a difference with testing. Also I never had a problem with the spark before I built the motor but I'll check the wires leading to the COPs just in case. The engine isn't running too rough I might add. Steady idle and revs, just audible misfiring pops.

When you say pops, do you mean a backfire?

I may have misinterpreted what you meant by misfire if you're saying there's no rough running condition, just exhaust pops.

A lean running condition could cause/accentuate a backfire.

Video of the car running for reference