Let me start by telling you that I pulled the carbs and cleaned them. Put new plugs and new rear tire. Never road a 1000f. So anyways i go out and ride about 50 miles, some twisty and some highway. Bike ride awsome. Stop at friends house 25 minutes. Get back on the road to go eat. Bike misses bad. Like it running on 3 cyclinders. I road about 40 miles back and stop to eat. Maybe about 45 minutes. Start home and bike runs perfect on all 4 cyclinder. Just messes with my mind how it runs so good and then bad, then good. But all in all great ride. Love the bike just need to fix some kinks. Thank Ez

 

Could it be our old friend the choke - causing one needle to stick open at times......?
Could be vacuum too as Steve-o says.
Or a simple loose coil wire.
Or a dodgy plug
Many options........

 

Of course my usual remedy too add to the list is .... dump some seafoam or any carb cleaner in there for good measure

 

I would go back and see what you have just done to your bike and check everything over. Who knows you might find something loose.

 

Try the seafoam Idea this happened to me and my ZX9 and it fixed it right up....other than that I would say a vaccum line like shadow said....

 

Glad to hear you got her out, tooez. As far as the problem, see above.

 

I hate to revisit my own threads. i took carbs off and everything looks good. All was tight. The only vaccum line I could find is the 1 that goes from number 1 cylinder to the tank. I replace it and still no running right. thanks Ez

 

Seafoam as mentioned above. I used this stuff in my tank for the 1st time ever & she runs stronger than before, this stuff works. Try it, it will loosen anything sticking in side. Report back after use.

 

Here a good update. I put sea foam in bike still ran like crap. I took carbs back off and guess what i found. One of the low idle jets was in the bottom of the bowl. I must miss tighting it up. All my fault. Bike runs perfect now. I got to ride it today and ran perfect. Thanks for all the info. EZ