I have an MS2, running an NB1 engine in a 94 chassis. I have run into an issue that I believe relates back to the #3 injector controller/driver.
This issue cropped up at the track. First session of the morning when it was cool outside( ~50*F) it ran with no issues. Second session of the day(~65*F) it ran mostly fine, had one or two times where it glitched out and ran 16:1 at WOT before it went back to normal. Third session of the day(~80* and climbing) it ran fine for two laps, then completely died, running 17:1 at WOT. All the rest of the day while trying to fix it, it was 85*F or hotter. Previous days have all been much cooler(60*F or cooler) and I never had this issue.

Car sounds like it's running on three cylinders and idles at 18:1AFR, if at all. Unplugging the coil for the #3 cylinder has no change in idle, unplugging any other cylinder causes it to try to die even more. Spark tests good on that cylinder. Good compression on all cylinders(215PSI). Swapped the #3 injector for a known good injector, same result. Shot wiring between the Megasquirt and #3 injector, wiring checks good. Megasquirt reads all cam/crank sensors properly.

Fuel rail is clear of clogs and has adequate fuel pressure. Car was tuned on a dyno last week without any fuel issue, made 157whp/129tq. The only thing I can think of that makes any logical sense is that the MS itself is heat soaking and acting up. The MS is located on top of the trans tunnel behind the dash(no HVAC, guttted dash). The trans tunnel has reflective tape on the underside under the MS's mounting location and a layer of foam between the MS and the trans tunnel, but I noticed the MS casing was still hot to the touch when I was shooting wires. The kicker is that after trailering the car home for two hours, it fired right up and ran normally(at that point night had fallen and it was ~65*F). This is arguably the hottest day it's been driven, while it seen some street use/mountain runs its not driven nearly as hard as it is on track.

I also sent an email off to DIYAuto, but interested if anyone here has some other suggestions.

 

I had a similar problem - it was uneven electrical contact in an injector electrical connector.
Somehow the problem appeared on very hot engine only.

 

I was unable to replicate/fix the issue by messing with the connection. With the engine running, I can push a long flathead down and push/pull on the connector- no change.
Also, the issue doesn't really seem to correspond to engine temperature, it comes and goes more with ambient. I can be pushing it hard on a 50* day and it's fine, but it crops up on an 80* day. Not that this motor runs that hot anyway, with a reroute/stock rad it stays 180*, fans kick on at 195*, never seen it go over 200* and that was while sitting in traffic for an extended period.

 

Update: Issue was found to be a broken solder joint inside the MS. One of the jumpers for cylinder #3 had come loose and was only making intermittent connection.