Motorcycle Repair: back firing and not idoling right, kawasaki zx9, spark plugs

Question
I have a 94 kawasaki zx9-r that through a rod so I had to replace the engine. the engine I found was a '97 zx9-rr. It starts and runs but it is back firing and does not idol corretly. It also runs poorly at low speeds. I know the emissions difference is 10.1 on the old engine and 11.3 on the knew engine. Is it carburater, coils, or spark plugs?  

Answer
Hi April,

Are you using the 94's carbsvor the 97's carbs? Which air box is used, or are you using individual air filters?

Describe the appearance of the spark plugs. I'll wait for your reply, then we can go from here.

Include your email address as requested. I'll send repair information files.

Respectfully,
Mark Shively