Motorcycle Repair: CB900C starting issues

Question
QUESTION: Hi there!

Purchased a CB900C in July of 2014, been working on it on and off since. Bought it with no starter, tracked one down and it still wouldn't start. Traced it to a bad ignition control module, so I purchased a new one and it started, but only cylinders 1 and 2 were firing. Thought I'd found the cause to be a bad ground wire, but that was temporarily repaired and still nothing on cylinders 3 and 4. I will note, when testing for spark on the plugs (it does have new coils, plugs and wires.), we would get spark and occasionally get a continuous spark on plugs 3 and 4 even after taking our hand off of the starter. Any ideas? Thanks in advance!
  Chance

ANSWER: Hello Chance,

If you haven't just write it wrong, then you placed it wrong...!!!
What I mean is that, the pairs aren't 1-2 and 3-4. It's 1-4 2-3. The coil with the Yellow wire
is for cylinders 2 and 3  and the one with the Light-Blue is for 1 and 4 (the Black-White wires are common).

In case you just wrote it wrong in your question, get back to me for further "investigation".

Best Regards,
Lazaros.  

---------- FOLLOW-UP ----------

QUESTION: My apologies, must not have re-read my question aha. But that is part of why I'm as confused as I am. Because cylinders 3 and 4 won't fire, and like you said they're both operated by two separate coils, so I don't know what could be the problem because it appears to be an electrical issue but I've checked everything except for the pulse generator. And that I don't know how to check unfortunately.

Answer
Hello again,

Since #1 and #2 are firing, there is nothing wrong with the pulser coils.
Also if #1 has spark, there is no way that #4 hasn't. Same for #2 and #3.

Remove all spark plug caps and check for spark straight from the wires.
If you have nice blue spark on all wires, then your problem isn't the ignition.
Could be the spark plug caps though...

I should suggest that you start with checking compression pressure on all cylinders.
Next, remove the carburettors and check for clogged jets.
I assume you've already checked if all carbs get fuel in the bowls...   

Get back to me with results.

Regards,
Lazaros.