Motorcycle Repair: Yamaha YZF 750 R (1994), yamaha yzf 750, carburetor jets


Question
My 94 YZF 750 R is misfiring on #3 cylinder. It's an intermitent fault and seems to get worse both when the bike gets warmer and the revs get higher.  The bike can tick over quite nicely and then when I take it out it struggles to accelerate, surging and spluttering.  
I've checked and renewed the plugs. Can the HT coils become faulty, or is that unlikely? Likewise could the main ICU be causing a weak/ intermitent spark on one cylinder. It's definately only #3 cylinder. Sometimes on starting the bike, I can feel the exhaust on no 3 cylinder and it will still be cold and the other 3 are to hot to touch. Other times it runs ok and they get hot the same.  
I have just replaced the engine with a second hand one from a breakers, however this same problem was happening with the old engine. (The old engine developed a valve problem on #3 cylinder, firing back through the carbs).
Any suggestions would be much appreciated.  

Answer
Hi Ron,

Awesome MC!

Q:  Can the HT coils become faulty, or is that unlikely?
A:  It's possible.

Q:  Likewise could the main ICU be causing a weak/ intermitent spark on one cylinder?
A:  Yes, this is possible, too.

It could be electrical or fuel related, or a combination of both.

Perform cylinder compression check to determine condition of combustion chamber sealing properties.

Perform electrical checks on all ignition components.

Remove and inspect carburetor jets and passageways for varnished fuel obstructions and rust particles.

Respectfully,
Mark Shively