Sounds like you have a sticking carb slide in the open position. Compare them when you pull the airbox and see if they are not even.

 

How do you exactly do that? check the slides?

 

Open the airbox and see if both of them are at the same location. Push them up and let them return. Are they at the same rate? Even a slight difference can mean poor running as you described.

To me it sounds like one is rising slower than the other but eventually opens up.

 

Okay so i took the tank off and i belive i had all of the hoses hooked up right on the fuel tank. i took the air box all the way off. so now i have the carbs completely uncovered. so i looked down into each carb and pushed each slide to the side and released them and they seemed to move at the same rate. so what do you do to check the petcock? also i was reading and someone said that if the diaphram has a tear of rip in it could cause it to what it is doing.

 

PVLIR? Petcock Vacuum Line Inadvertant Relocation? If vacuum line is hooked up to bottom nipple that is wrong. Should be on nipple towards back of bike.

 

Also, make sure it's the right line hooked to the petcock. I can't believe Honda put two identical lines so close together.

 

If he can run WOT the petcock don't starve the engine, I used to check what have been disturbed by a mechanic first in those situations. The jets are located under the carb, what you see is vent holes. You need to take them off completely, unscrew the bowls under them to get to the jets. So unhook throttle position sensor, throttle cables, coolant lines, unscrew the boots and pull like mad, be careful not to pull on the linkage or sensitive parts. You may want to check the plugs first to see how they looks, if you can post a picture it would be nice, a lean out would shows from whitish carbon.
It could be valve timing, but the bike would idles rough and die sometime. Are the symptoms RPM dependent ??

 

The bike idles fine. And when im pass 1/2 throttle it seems to run okay. but from pass idle to 1/2 throttle it seems to surge and miss. Also when i have the bike idling and i rev it up it pops and backfires. Now it has never done that while accelerating. It has poped and backfired when down shifting. But that is normal. So at a kinda high RPM it seems to run okay... But at a low RPM it runs like crap!!!!!!

 

WOW finally think i figured it out... Even though Hawkrider and Brian A said it from the begining. Pulled the carbs and checked the jets and bolth pilot jets were clogged. so cleaned them real good and put everything back together. Took the bike out for a spin and wow what do you know back to normal! The only crappy thing is while hooking everything back together i over tightened one of the choke cable nuts that screws into the side of the carb and it broke off!!! So half of it is stuck in the carb and then the rest kinda dangles out... So now i have to order a new one! But overall runs good! Hey thanks for all the help guys!!!!!!!!!!!!