2017 F90lb no start

[SSkaiman]

Hi Guys-I've been checking out the site for some time now as a guest. You all seem to help a lot of people. I have what I believe to be a doozy. I have a 2017 F90lb which was running fine until out of the blue it stared vibrating a lot and i had to limp home. I left the boat with my son as i was on an extended trip and he tried to get it running at the marina but it would start only briefly vibrating the whole time. It then died and would not start at all. Someone who claimed to be a mobile mechanic was there and he said he was sure it was a fuel delivery issue. He worked on it and eventually said cylinder #4 wasn't firing so he replace the coil (twice). When this didn't work he ended up changing the ecu for a refurbished one. He got it running a couple of times on the trailer but each time it was tried in the water it acted up the same way. I don't think he knew what to do. It now either doesn't start at all or sometimes fires for 1-2 seconds.
I recently got home and due to the frustration with the mechanic I tried my hand at it. I ran thru the yamaha service manual crank no start and irregular idle troubleshooting procedures. I also have ydis 1.33 but it acts erratically losing communication with the ecu and claiming the boat is running or in gear in some stationary tests (tps voltages within spec). It also won't let me run engine monitor. (I had the chipped obd2 type cable replaced but no luck)
I went to the ignition system first since the mechanic was messing around with that. I found that both primary and secondary coil resistances were ok. Spark plug caps resistances also ok. Did spark gap testing and found no spark at cylinders 1/4. (2/3 ok). Switched coil connectors from one to the other and got 1/4 to spark (2/3 no spark). Seems like there's no signal to fire to coil for 1/4 input voltage is ok. Continuity between coil connectors and fusebox and ecu all cylinders ok.

Pulser coil resistance ok (which it would be if I understand batch fire correctly and i have spark at 2/3)
Went to the fuel system troubleshooting to be complete and injector resistances all fluctuate from 16-24 ohms (weird? for all to be out of spec and fluctuate-low battery on multimeter maybe? I was able to fire injectors 1 and 2 with ydis (with 3/4 it said engine was in gear) Also able to fire electric fuel pump with ydis. It gets weirder when I checked injector continuity. 2/3 had continuity all along circuit to ecu but 1/4 had no continuity to ecu. I thought ok I'm onto something now-but upon checking the wiring diagram closely i noticed that the ecu connector pins positions for the 1/4 injectors and the water in fuel sensor were switched. When checked for continuity with the correct wire in the wrong pin position (per manual) I got continuity. I don't know what to make of this-it seems awful coincidental that these are the same cylinders I'm having spark issues with. I don't know if the manual is wrong or the old ecu is supposed to have this wiring configuration. It would seem then that changing the ecu to a new one with the manual's stated wiring would cause troubles-but i don't know. I would guess that the manual is simply wrong but what a coincidence that it would be wrong with injectors 1/4' s wiring.

Fuses,relay to ecu and ecu to ground continuity ok
Pulser air gap ok
pulser coil to ecu continuity ok
fuel hose ok
fuel filters ok
high pressure fuel pump ok
valve timing ok
isc valve checked resistance ok but can't verify function on ydis
throttle valve ok
spark plugs ok
fuel pressure >40 at rail
injector input voltage ok

Was not able to check pulser coil output voltage-no dva
Also not able to check compression-no tester for this engine at hand

All I can think of if compression is indeed ok is that the ecu is bad. Aside from the service manual checks (which checked out ok), I don't know how to confirm that it is bad. Maybe there's something I'm missing that you smarter guys can figure out

Thanks

[Queequeg2]

"2/3 had continuity all along circuit to ecu but 1/4 had no continuity to ecu. I thought ok I'm onto something now-but upon checking the wiring diagram closely i noticed that the ecu connector pins positions for the 1/4 injectors and the water in fuel sensor were switched."

If it was running okay and then just quit, I don't see who wires could suddenly be switched.

[SSkaiman]

My thinking exactly. Most likely the wiring diagram is simply wrong. But because the ECU was changed, maybe there is a different ECU with a different wiring configuration for this same engine model. In that case, there would have been a separate problem at the beginning that may or may not have been corrected and now the ECU is wrong. Much more complicated and less likely I know but the coincidence with the 1/4 cylinders being involved is just weird

[ausnoelm]

So much has been fooled around with it will be difficult to just get it back to the stage where it’s just broken……..I don’t understand the trouble shooting, you know you have no spark on two cylinders, but you move on to the fuel system? How does that make sense? Do you still have the original ECU?

[SSkaiman]

I basically followed all steps listed in troubleshooting no start but cranking. Found and could not explain no spark in two cylinders. I still can’t explain it. Went on to check fuel system simply to be complete and check everything. I do think it’s an electrical issue and wasn’t expecting the fuel system wiring weirdness. It may not mean anything though. Why not check everything while I’m running troubleshooting. Only the 1/4 coil and ecu have been changed. The original ecu ended up a a core

[Queequeg2]

It sounds like you are trouble shooting through parts replacement. It's easy to fall into this trap and it will get expensive fast. I believe it was a mistake to start swapping wires around. You might risk burning your new ECU. Don't see how one ECU would have a single pin difference. I wouldn't have changed them.

When you got the "Engine in gear" error from YDS, did it also say, "or might be running"? When I get that error, it's the USB cable and nothing to do with the engine. Sounds like the same for you. If you are using a USB cable extension, remove it. You can't count on YDS if you have an erratic signal.

"Switched coil connectors from one to the other and got 1/4 to spark (2/3 no spark). Seems like there's no signal to fire to coil for 1/4" Doesn't this tell you what you need to know? One way you can eliminate fuel issue is to get a small spray bottle and put gas in it. Open the manifold and spray some gas into it. Then see if the engine fires. If you eliminate fuel and compression you can focus on electrical. Did you try to bypass the kill switch?

[SSkaiman]

Maybe i'm not being clear. I have not switched ecu wires around at all. The pins remain original. The coil input wire swap was temporary simply to see if coil 1/4 would fire. It did. The coil input wires input put back in their original connectors after the test. Can anyone explain no spark in just 2 cylinders? Bad ECU? Kill switch was bypassed and no change. I actually don't think it's a fuel problem-I just mentioned the wiring diagram irregularity as a weird thing I found. It's just strange that that wiring discrepancy involves the same cylinders I'm having trouble with.
According to Rodbolt17 every time he's see the engine in gear or running error it was due to a TPS. Mine is in spec per the service manual so I don't know

[SSkaiman]

Does anybody have any ideas?