No spark on 1 cylinder

Hi all. I've a problem that has been puzzling me for a few months now. I hope someone will be able to point me in the right direction.

Last year I bought vz800 m800 2008 which I planned to use as a project bike. However, the plans have been ruined by electrical problems. When I bought the bike, it was running just fine, however, occasionally it was cutting off usually soon after the bike was started. After starting again I could drive for hours with no issues. 

This year in April I took the bike for Mot. On my way back, the bike misfired a few times and for the first time died while riding. I managed to start it up again and drove home. Started reading what could the issue be and found that it could have been caused by ignition coils. I bought 2 new coils, spark plugs and new ht leads, replaced and took the bike for a test ride. 600 yards from my home the bike misfired and died. I managed to start it up again but it was running only on one cylinder.

With my mate who is very good in fixing bikes we found that there was no spark on the rear cylinder. I got myself the service guide and started going through the Ignition problems chapter. I did all the tests described in the chapter and all the tests were OK, I mean confirmed that the coils, cpk and other elements were OK. Everything indicated that it could be ECU.

I bought a replacement from USA, put it back in and the bike became alive. I was pretty sure it was the end of my problems so I put the bike back together and went for a test drive. After 4 miles, the bike started working on 1 cylinder again! Came back home on 1 cylinder, checked the spark and found that this time I had no spark on the front cylinder.

Since then, I've checked pretty much everything to find what the issue might be but it is beyond me and my mate at this stage.

What we did:
We measured continuity on wires going to the coils and resistance and it seems to be ok

Replaced the female connectors which are attaching to coils to make sure there is good connection. 

Checked point of contacts of the wires that are in use in the ignition system

Checked kill and start switch 

Checked and replaced kick stand switch

Checked CKP and voltage is over 5, resistance in the correct range
 
Checked voltage using peak voltage adapter on coils and wires from ecu and here is where things get complicated. 

Using the peak voltage adapter i can see the voltage between black yellow wire and orange white is on average 1.5v on both coils with the spark cap off the plug. With the cap on the plug the back cylinder shows around 160v and front cylinder nothing. When I measure plus on the coil to the ground, the multimeter shows 11.8v where on the battery terminal is 12.5v. I'm not sure if this supposed to be like this but I would expect 12.5 on the coil as well?

The voltage is coming from the ecu so I'm guessing the ecu is still functioning.

Has any of you have had a similar problem and would be able to shed some light on it, that would be great.

Regards
Paw

Assuming it is the same as the VL800 (and I'm sure it is) the ignition is what is called a lost spark system, so both coils fire once per revolution meaning one cylinder fires at the top of the compression stroke and the other fires at the top of the exhaust stroke.

If you are getting pulses from the ECU, you should be getting sparks from the coils. You need a spark tester of some sort, so you can physically see the spark, but knowing how deep into the 'heads' the plugs are, it may be a bit of a bugger. Beyond that, I'd be using my digital storage oscilloscope, but that's a very specialised piece of kit...

Mine VS800GLS M800 ,Was the CDI Unit under rear seat. Run great now.
John.

Thank you for your replies. I've just ordered the wiring harness from states at fairly good price. Will also buy another cdi. I found a brand new on ebay and I think I'll give it a go. Hopefully third time lucky...