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S2 Crank but no start. Low d09

I will do that. I will also check voltage drop between battery + and coil positive supply.

New spark plugs and eBay coils are on their way too.

Voltage drop between battery- and chassis is 0.014V so the main ground seems ok. Even though I have improved the ecu ground (voltage drop from 0.25v went to 0.07v with extra wiring) I would like to check all other grounding points, but I can't locate any. The only one i have found is behind the instruments cluster (S2 half fairing version). There are two grounding "spiders" near the ecu which I have cleaned but I was not able to locate and follow the wire that actually goes to chassis. Any other known grounding points?
 
I fitted a new battery.
Voltage drop between battery positive and coil positive is 1V. It should be lower IMHO. I also replaced the spark plugs which I gapped at 0.6mm - 0.65mm. I also installed a set of used coils I ve got from ebay. I cleaned the caps interiors and made sure I have connectivity as shown here

The bike started instantly but I am getting misfires on cylinder 4. Same cylinder I was seeing intermittent sparks with the spark tester.
Cylinders 1,2,3 have approximately the same temperature while cylinder 4 is about 90°C cooler. What does this tell us
1) bad command from ecu? ( should #1 have the same issue?)
2) bad HT lead ?
3) bad connection between HT lead on the cap or cap - spark plug? Ceramic resistor is in spec.
4) bad coil ?

 
Number 1 and 4 cylinders should have the same spark so I doubt it's an ECU control issue. Sounds like a big gap between the coil HT wire to number 4.
Maybe bypass the ceramic resistor for a test.
If it's possible to swap the 1 and 4 HT wires for a test.
 
Number 1 and 4 cylinders should have the same spark so I doubt it's an ECU control issue. Sounds like a big gap between the coil HT wire to number 4.
Maybe bypass the ceramic resistor for a test.
If it's possible to swap the 1 and 4 HT wires for a test.
All caps were dismantled, cleaned and tested for continuity before fitting. Back screw, spring, resistor = exactly the resistor value, end brass terminal and spark plug contact = 0 ohms. Caps are ok, firmly screwed at the ht lead of which the inner strands were exposed, straightened and cleaned before screwing the cap. My car mechanic suggested to swap injector 4 with 3 for example to see if the cold cylinder moves. What i haven't be able to inspect is the ht lead connection to the coil side. I chickened out removing the holding clip.
I can always put back the old 1-4 coil to check the temperatures, I should have tested this before, but i haven't. I still have much to learn.
 
Switching Injectors sounds logical except I thought you were experiencing a spark issue at #4 but not #1
 
All the spark tests i did in the past while the engine was refusing to start were on #4 due to accessibility ease. So i can't be sure if I had missing spark on other cylinders too.
 
Today i tried to track down the 1V drop from B+ to coil positive.
I have 0.4V drop from B+ to red/white on the cutoff relay (0.25v of which is due to ignition key switch). Another 0.35 from red/white to red/black (kill switch). The rest is fuse contacts, cable loss, plugs. I tried to clean the kill switch. On the street. Late afternoon. Got dark before realising it. Daaang... ball and spring flew away. Could not see my nose. Found them and put everything together... went to hell and returned.
 
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For 10 days after replacing the battery and the ignition coils the bike was starting just fine. Until yesterday, same issue. I visited a new mechanic, gave hime the whole story, showed him some videos and his opinion is that i have to check the starter motor. He asked if i have ever replaced it or repair it (never replaced, brushes replaced a year before this issue appeared) and seemed weird to him that i have 98.000km with the same starter, since the only frequent failures the fz6 that he has faced were the magneto and the starter motor. He also noticed that in cases the engine started there still was a delay of about 1", it should be quicker. He is not fond of aftermarket brushes, has seen cases of creating bad connection or nearly shorting (thus creating the voltage collapsing making it seen like a mechanical lock that i am facing every once in a while). Regarding the missing sparks he said that if due to bad brushes if the motor spins with less rpm (not noticable by ear) the cps signal will be weaker (perhaps any residues or debri on the sensor makes things a little worse). On the other hand i am seeing a clear signal on the scope. He suggested a push start next time to verify the theory, which was also mentioned in this thread also.
 
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