2003 Kawasaki zx1200c motorcycle running rough

Not really enough information to help. What kind of motorcycle, what engine? Is it a 4-cylinder or 6 cylinder? Does it have a carburetor for each cylinder? You have spark on one and two, but it won't run? Could have no spark, or you could have carburetors not giving you fuel.

Any one of these could be cause of your problem. Sounds like maybe a spark plug coils is bad. Did you gap the plugs? Also sound like secondary fuel injectors not opening fully, and air leaks inbetween intake boots and head. Start bike and let idle Use non-chlorinated brake cleaner spray small squirt on each intake boot find the leak when the bike idles up there is a leak. You can't properly sync multiple carbs if there is even one vacuum or intake leak. Take out spark plugs keep them in their own same cylinders. Read the plugs what do they tell you. Google how to read a spark plug.

There are 3 components necessary for any motor to run-fuel, air(compression) and spark. Just because you have new plugs doesn't mean you have spark. Put them in the caps and ground them to the cylinder head and turn the motor over and look for the spark. If you have spark, install the plugs and plug wires, and turn it over several times. Pull the plugs and check to see if they have fuel on them. Run these 2 simple tests and get back to me with the results and I'll help you further. Good luck!