Your issue is eerily similar to mine. very small gapped helped me too, but only temporarily. I suspect that once you get some more miles even at that .010 gap, the problem may return for you too, hope i'm wrong though. On my setup once plugs got any color the problem quickly returned even with a very tight gap. If you watch the video attached, particularly from about 9 minutes and onward, that is the part of video that gave me clues to fix my setup. Apparently mine was emi related problem from the ignition system getting into the crank sensor wiring. Emi from ignition sources will be worse at higher boost and loads. Smaller plug gap, resistor plugs, spiral core wires all help with emi but none of those completely mitigated issue for me anyways. See my post above on what I resorted to fix problem on mine. Basically took a noise filter capacitor on the coils power and shielding and rerouting sensor wires away from ignition and other high current sources.

Although this video is geared towards ecu grounding, its the info from around 9 minutes on that gave me clues to fix my setup.

 

Your post was a good read. It does sound like similar issues, at least from the RPM readings. None of my other data logs has anything real funky going on with the RPMs so I am feeling alright about it for now.. When I stared my build I was having issues with the CAS signals getting to the ECU (wiring issue) and during that set up I shielded and grounded those signal wires. For my current set up from testing and trying a bunch of things, I have my coil power, ground, and signal wires fed from my passenger airbag cavity (where my ECU is mounted) up over my windshield and into my engine bay (no hood right now). LOL. It is quite a sight to see as a spectator and if the car didn't turn heads enough before, it certainly is now. Last week a kid shouted at a gas station "WHERES YOUR HOOD" lol. But because of this wiring situation I feel pretty good about my coil wires not being interrupted by EMI. There is a good distance between the wires unlike being in wire loom together. The CAS wires that I use for engine position are still in relatively OEM configuration though so I could be getting noise there, but then again they're shielded and grounded, just no filter.

I have done a decent wire tuck on my engine bay, most of the wires are in the fenders and I would hate to re-tuck it to separate power and signal/sensor wires. I would if I needed to.
I feel like the Speeduino could be more susceptible to noise than a Megasquirt OR you had some electrical gremlin playing evil tricks with you. But this disposition would be based purely on price between the two so I could EASILY be wrong.

I have a TERRIBLE atmosphere now for EMI and my problem did not get worse doing creating this atmosphere. In the spring (when this problem came on) I had MSD resistor core wires meant to help dampen EMI, and standard NKG resistor sparkplugs also meant to dampen. When I suspected a weak spark I put non resistor core sparkplug wires in, which dropped the resistance from I think 3,000 ohm to 30 ohm per foot. And tried some non resistor sparkplugs. Both of which help have a stronger spark, but do not help EMI possibilities. And I did not experience anything worse (or better) with my breakup issue, or anything looking weird on the data logs like my RPMs.

I will keep this in mind as I move forward as I test other coils and hopefully am able to open my gap back up.

 

Have you tried a capacitor on coil power yet? The old online megasquirt instructions mention adding capacitors to the gm coils.

My cam and crank wires were also shielded from day one of install. When I decided to really go after the problem I was having i decided to move and shield all the low current signal wires. I'm not sure which wires were transmitting any ignition noise, I just went after all of them at once.... One of those wires was basically acting like an antennae back to the ecu I believe. I do know high current power and low current signal wires should not be bundled together. Good practice is to separate. I know the capacitor on the coil power helped as well...

Also might want to consider 2 separate 12v supply wires all the way back to the battery.. One to power the high current "dirty" power for coils, injectors, solenoids etc. And a separate power supply to give "clean" power for things such as the ecu and any 12v powered sensors. The battery can act as a giant filter too.

Emi is not just a speeduino deal, I helped a buddy out with a holley terminator x that had to fix a couple signal issues too likely from emi, his was easy to fix, mine fought all the way LOL..... However you could be right about me having an electrical gremlin that I had to work around, my wiring is ugly.

 

I can be the coil, the plug, the plug wires, the dwell setting, the AFR, the timing.

My guess is coil or plug wire. To Newaza's point, if it is a bad coil or wire, as soon as that spark jumps straight to ground instead of firing across the plug, that can wreak havoc on the ECU inputs. I've seen that where it's loosing sync because of it, but a bad coil or bad plug wire was inducing the noise that was then causing the sync problem.

My guesses in order would be coils first, then sparkplug wires. I once had a good set of wires that I knew were good (name brand, maybe 1-2 years old max and not many miles) but finally just wrapped them in several layers of electrical tape to prove they were not the problem. It immediately fixed my misfire problem, proving my good NGK wires were not good-enough!

I now run some crazy sparkplug wires.Photo - Google Photos

 

this is another good read. They surmised were basically getting induced emi from high current power and power for crank sensor being bundled together. they cured by relocating the sensor power and ground wires away from high current power.
https://www.springbokphotography.com...r-interference

 

Well it took me several days to get to the car.. why does life have to get in the way? I just wanna drive my car lol.
I tried some new coils at 0.020" sparkplug gap, and the problem was still there. I was surprised because the 0.010" gap on the stock coils had worked which made me think I had a weak coil. So I put the stock coils back on the car, and then investigated the wires. As I was driving into work yesterday I realized I may have been causing an issue. To make a long story short, when I made my new spark plug wires a few weeks ago I did not have one of my sparkplug boots. So I used a standard LS one. Attached is a picture to how I had it installed.. I believe I did not have the boot in the correct spot in relation to the sparkplug. I thought that maybe when boost pressure built, and my cylinder pressure reached a certain amount, then the electricity coming down the sparkplug wire had a less resistive path, and that was to jump from the sparkplug terminal onto the cylinder head 3/8" next to it. Because it wasn't insulated.
Last night I removed the LS style boot and put on the factory style (the coil side rubber boots are flowforces from the original kit). I was able to do several pulls without a single break up, and then 2 pulls had one little hiccup in the middle of them.
Then later last night, I took my car out for another test drive. Only for the problem to be back full force. UGH.
I am going to investigate the wires more as this was the first time I had been able to build 23psi with a reasonable gap. I am going to try electrical taping all the plug wires like Pat did after I make sure that the terminals on each sparkplug wire look proper.