I have still not resolved my misfiring problem on my new built 3.2SS with 9.5CR and Webcams 464/465. Dual EDIS waste spark ignition with one VR sensor to both of the EDIS ignition modules (dual spark). One ignition system runs upper plug set and the other set runs the lower plugs. PIP to ECU from one ignition module, and SAW from ECU is split to both modules. MS3X ECU batch fire injection. I still have the misfire on #6 cylinder at idle and low loads. It runs fine with more load and RPM
1) Leakdown on all cylinders 2-3%
2) Compression tests on cold engine
cylinder #1 - 165psi
cylinder #2 - 165 psi
cylinder #3 - 160psi
cylinder #4 - 180psi
cylinder #5 - 165psi
cylinder #6 - 170psi
3) Plug chop; all plugs indicating lean except both #6 plugs which are both much darker and wet
4) Checked for false air (including loose manifold and hoses)
5) All twelve plugs spark nice blueish
6) Checked opposite plug #3 that is running off same coil. #3plug has fine color (#6 is wet) - so coil pack should be fine
7) Stroboscope shows stable spark on all 12 plugs, with identical timing
8) Runs equally bad on only upper ignition circuit only and on only lower ignition circuit
9) No noise on MS log files, except for the obvious fluctuation in AFR signal caused by the misfire
10) Replaced all spark plugs - no change
11) Replaced all spark plug leads on upper plugs/ignition circuit - no change
12) Tried separate power&ground direct from battery to ignition - no change
13) Tried running fixed 10 degree advance (SAW disconnected) -no change
14) Disabled Accel enrichment entirely, to prevent fuel dumping from noise or pressure fluctuations - no change
15) Tooth logger and composite logger in Tunerstudio look fine, but tried adjusting on the pot meters anyway -no change
16) Swapped injectors around, flushed and checked spray pattern- no change
17) Tested with different injector dead times - no change
18) In ECU test mode all injectors can be tested individually and all 6 are cycling and clean opening signal on the oscilloscope - so no bad connections to injectors
19) However with the engine idling injector opening signal to cylinder #6 has noise, an additional spike at as the injector closes
20) Swapped in a set of much smaller injectors, to get longer opening times and less influence of the error - improvement and was able to go on the annual Fjordluft event after all
21) Plug chop on return 500 miles later has 5 lean running plugs and #6 still too rich

What to look for to resolve the noisy opening signal to #6 ? All injectors have common 12V supply and individual switching ground in the ECU.

You may be onto something to look at the noisy signal on your #6 injector.

One thing you can look at if you haven’t already, is what’s different about the wiring/harness for that injector. Running close to a sparkplug wire or coil, bad ground, etc. SOMETHING is different than for the other cylinders.

Also, might be worth getting on the Megasquirt forum - there should be a ton a knowledge there for random yet not uncommon issues like you’re having.

When you swapped the harness, that included all the leads to the injectors, right? And you've moved the injectors too and the problem stays with cylinder 6? And you replaced the ECU and the problem remained with cylinder 6?

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I would put another 1000 miles on the motor and make sure its broken in before I would take it apart. Maybe it will self correct.

Before you start taking apart the engine, get an inspection camera that connects to your phone, that you can insert through the spark plug hole and take some pictures.

At this point, those are cheap enough that everyone ought to have one in their tool kit. They are extremely useful for many other applications too,

I am embarrassed to say that my engine running issue seem to have been related to me not having set up the ECU correctly for the RPM signal.
When I ordered the MS3X I had it set up from DYIAutotune for VR sensor. But when I finally got around to installing it with EDIS some 4 years later I had completely forgotten, and for some reason I don't want to discuss I did not check and re-configure jumpers on the board.
Nothing wrong with engine after all. Engine now runs on CDI/distributor ignition and is smooth as silk and powerful. It idles stable at 1000 rpm and 7 degrees advance. There is still a stumbling issue between 1500 and 3000 rpms, that I am confident I will be able to iron out, but above it is smooth as silk and has good power

Thanks for the follow up.

Good to hear you got it sorted out. Lots of variables with the MS system.

Good you got it sorted