HELP, please !!! 3rd fried ECU !!! Would wrong ECU just fry it or not run at all?

On my 2nd harness. I completely isolated the new harness. With the red wire marked 12v to kill switch, blue ignition wire to switch on dash and starter wire to starter button. I have the fuel pump wired directly to harness wire marked fuel pump hot. I removed fan, water pump , power commander and gear indicator wires. I've paid several mechanics and all have different ideas on what the issue is. I spent 4 hours with a mechanic yesterday and something strange occurred, the red 12v wire had 12 volts coming out of it!! WTF!!! The 30 amp fuse blew, we changed it and it no longer had power coming out of it for the rest of the day.

I'm going to cut open this harness tonight and see what I find, the last one had some melted red wires by the starter relay. If I were you I would do the same before you fry another ECU.
 
I did not find any melted wires on the 2nd harness but the fuse on the starter relay was blown. The 1st harness did the use the busa start relay, so I assume the busa relay/fuse saved this harness. But it still does not explain why it runs on whatever 2 cylinders it feels like.

Have you put a noid light to the injector plug on cylinder #3? Have you pulled off the throttle bodies and crank the motor to see if injector #3 fires? How about a compression test on cylinder #3?

The reason I ask is when I pull the fuel rail and crank motor all 4 injectors fire. If I attach fuel rail only 2 fire. If I pull throttle bodies 3 injectors fire. This makes no sense to me at all, driving me nuts makes me want to drive this race car on 2 cylinder into the nearest lake!!!!
 
I spoke with Peter D (guy that answered phone ... not their guy that does the wiring mods) and they mentioned very weird things can happen if you mix up two of the wires on the starter relay yet can still run but confuses the ECU whatever that means. I am not sure if this applies to either of us but something thought would throw out ... maybe even you have been talking with them and this statement is related to your case. I am in Phoenix so if this next rounds of fixes blows another ECU its getting dropped off at Peter D.

My #3 clylinder looks fine except not firing the injector. Switch injector plugs over from #2 and #3 fires fine but then #2 is down. Mine seems fairly cut and dry that the ECU channel for #3 is damaged/dead. We did check compression again on #3 as my mechanic was initially concerned as he also just replaced head gasket so wanted to make sure all was good and it was.

Maybe yours could be fuel pressure regulator or clogged injectors? You running a 40 micron or less fuel filter? I dont really know but just throwing out ideas.
 
My car was wired wrong and I assume so is yours. The red wire marked 12 volts was actually hooked up to 12 volts. So last night I connected it to the ignition switch and car started right up but running on 3 cylinders not 2. #3 not firing!! So I assume something in harness is fried. I ordered new harness and ecu to start fresh. Let you know what happens. I think your wasting your money buying ecu's without looking at harness replacement and/or looking at how your car is wired. I assumed guy I paid to wire the car knew what he was doing! Wrong!!!
 
Update. Original ecu is only firing on 2 cylinders and when I installed my spare ecu car is running on 3 cylinders with #3 not firing. Dont install the new ecu without checking how your car is wired and/or looking at the harness.
 
Update. Myself and eschmidt155 have been working this daily and I had a few more rounds of visits to my mechanic to replace (includes new injectors)/check various things, speaking with Peter D about the harness, and even some contact inside Suzuki but was just about to give in.

Long story short, think found root cause !!!!!! If I unplug the Air Intake Pressure (Boost sensor) my #3 wakes up and temps are fairly even accross all. Baffling how this sensor has so much effect on the ECU and does not even throw a code when apparently values are so far out of whack that it is shutting down cylinders. New sensor on order. Mine is rigid mounted to the engine block so thought is vibrations, heat, or similar might have got to it as it normally sits on the air box.

I was all the way up to my 5th ECU for troubleshooting purposes. We have now also tried these ECUs in street bikes and they are just fine so atleast get to recover some money here.
 
Standby ... its looking like it not actually the sensor for root cause (but certainly could be for others having a similar problem). The one thing I had not checked yet was if I simply disconnected the vacuum line fromt the sensor if it then works. Mine does! So, looking like it is something in the vacuum line routing/pair valve mod most likely. Will start a new post on this ....
 
Update. Received new modified harness from another company with long history of working with Busa motors. Same crap, motor picks what 2 cylinders it feels like running. He tested harness before he shipped it to me and it worked fine. Only difference is that I have a bullet fuel rail.
Could this cause interference with injectors since stock fuel rail is plastic where it attached to throttle bodies? I also now have a "CHEC" error on gauge cluster and I am unable to put into dealer mode.
 
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