Hey there, Don't mind those two, they do get a bit grumpy every now and then!
Okay, each coil fires both wires at the same time for that respective coil, so that's why you can just switch the 2 and 3 plug wires/caps to opposite cylinders, and will fire correctly. This technique is to see if the problem is Electrical...the problem will follow the wire and # 3 will start having problems and misfiring. BUT if it's a CARB issue, then #2 will still be problematic, and the #3 will continue firing as usual.
Fuel in the carb throat/air box is signs that the carb is still flooding, which can fuel fowl your plug and cause the miss. You say you checked the needle/seat. Aside from a piece of crud getting stuck/wedged in between the needle/seat, the actual float can also just get HUNG UP/stuck for several reasons. Either corrosion on the float PIN so that it doesn't swivel properly/easily, or even a new thick/wide bowl gasket that catches the side of the float keeping it from moving.
Also, did you clean the carbs, and did you use a Carb Kit ie. K&L brand??
Their parts are known to cause problems/issues, the float needle is designed wrong and can allow the flaot not to seal properly vs. Original Mikuni parts.
IF the pick up coil wires were breaking, they usually cause a miss in 2 cylinders because they cause an entire coil to loose fire, not just 1 plug!
From what you've stated, my money is still on problems with the carb/floats more than the wires/coils....VF1000 coils are just fine!
There are other more rare conditions that can cause loss of spark on just 1 clyinder....ie. the resistor in the plug cap can go bad, or get too much corrosion on it causing it to not fire, or fire with very weak spark.
T.C.

Okay, each coil fires both wires at the same time for that respective coil, so that's why you can just switch the 2 and 3 plug wires/caps to opposite cylinders, and will fire correctly. This technique is to see if the problem is Electrical...the problem will follow the wire and # 3 will start having problems and misfiring. BUT if it's a CARB issue, then #2 will still be problematic, and the #3 will continue firing as usual.
Fuel in the carb throat/air box is signs that the carb is still flooding, which can fuel fowl your plug and cause the miss. You say you checked the needle/seat. Aside from a piece of crud getting stuck/wedged in between the needle/seat, the actual float can also just get HUNG UP/stuck for several reasons. Either corrosion on the float PIN so that it doesn't swivel properly/easily, or even a new thick/wide bowl gasket that catches the side of the float keeping it from moving.
Also, did you clean the carbs, and did you use a Carb Kit ie. K&L brand??
Their parts are known to cause problems/issues, the float needle is designed wrong and can allow the flaot not to seal properly vs. Original Mikuni parts.
IF the pick up coil wires were breaking, they usually cause a miss in 2 cylinders because they cause an entire coil to loose fire, not just 1 plug!
From what you've stated, my money is still on problems with the carb/floats more than the wires/coils....VF1000 coils are just fine!
There are other more rare conditions that can cause loss of spark on just 1 clyinder....ie. the resistor in the plug cap can go bad, or get too much corrosion on it causing it to not fire, or fire with very weak spark.
T.C.
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