ninja zx600 running with a bog need help

i have a 2001 kawasaki ninja zx600 and it used to run great and has about 20,000 miles on it. ive owned it for about a year now and the only thing not stock is the exhaust when i bought it, its really loud and its pretty much two huge cans, its ran great until about a week ago. when i start it it runs fine, when it warms up and i begin to go it feels like its kinda bogging down. and sounds really weird, then after like 4,000 rpm it goes back to normal, then the idel is acting weird when at a stop and in nutral. then some days it never does it. then sometimes i start it in the morning and it doesnt do it at all and i ride it to like the store and park it then does it the whole way back. any ideas are apricated, im pretty new to bikes bit ive worked on cars for a long time. please help. i cant afford to take it into a shop so i need to do this work myself. thank you!
Chris