Rear cylinder not firing (SV650SY - 2000)

Hey guys, so I'v tried all I can think of to sort this out here.
Problem started a while ago, with my rear cylinder first cutting out but coming back to life while running. Then after a day of sitting, just flat out refusing to start at all.
Now I narrowed things down, finding that I wasn't getting any sparking from the rear one (With any sparkplug). So I got myself a replacement HT Coil, which I have just fitted a little while ago. Came to check, and still nothing.
Now I'm sure it's not this coil, as it came from a working SV650.
Could there be the possibility that it's an issue in the Ignition Control Unit? Or is there something else that could be causing the issue?
Thanks muchly in advanced.

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Have you checked the Carbs, if they are gummed up it could effect the running of one or both cylinders.

Defiantly not a carb issue
I have no spark coming from the rear spark plug at all (Which I did mention in the original post)
It's confusing me to no end.
The front cylinder is running fine. It's just the rear one which won't spark.

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Sorry missed that bit, have you swapped leads front to back, that would show an issue with the lead (not sure if you have replaced it) if you have replaced the coil then it may just be a case of getting out the multi-meter and wiring diagram and working from the spark lead backwards through each component and connector checking continuity and voltages.

My buddy's ECU went down and stopped the rear cylinder from firing.
It was proven by moving the two coil wires at the ECU plug itself and the problem swapped to the front cylinder.
Might be worth a try?

They are fiddly to move but can be done with a small flat screw driver.

If it's never had new plug wires (HT leads), which is likely, put some on. They don't last forever, and if one hasn't gone bad yet, it will. I used generic leads from an auto parts store. Just bought two that were long enough and cut off the end connectors.