I’ve looked through previous threads for this problem but haven’t found exact matches. Please direct me to the right thread if this is redundant. I’ll try to be detailed. Any help will be appreciated
Symptom 1:

Below ~170F, between 2,500 and 3,000 rpms, and at steady throttle the bike randomly decelerates for a nano second and then instantly recovers and has an associated clunking sound. The sound comes right after the bike seems to misfire (that would explain the studder). The clunking sounds like a cam chain slapping and seems to be the result of the engine misfiring? Maybe the carbs are backfiring? Now that it’s winter it’s more frequent since it takes longer to warm up. IF I HOLD THE CHOKE while riding it goes away and runs smoothly.

Symptom 2:

Between 3,000 and 4,000 rpm the bike seems to have decent torque and response. Between 4,000 and 6,500 it increasingly hesitates until it feels like a 250cc machine. At 6,500 it sparks to life and even at ½ throttle there’s no way to keep the front down. The power continues to 10,000 rpm with no indication of the power tapering off. It actually feels stronger than I would have expected from a SH – closer to the feel of my previous bike, a ZX12R, than the 105hp these things supposedly have.

Bike Specs:
-’99 bought two months ago with 7,500 miles and now has 9,000 miles
-Just replaced air filter with a Honda filter and replaced the vent filters too which were completely disintegrated (I cleaned the remnants out of the carbs)
-Manual CCT’s were installed by previous owner
-Smog removal completed by previous owner and everything seems to have been blocked off correctly
-Cleaned the carbs and everything looked brand new. I didn’t pay attention to the size of the jets but there’s a chance they are not stock (I’m sure I’ll be taking them off again to check).
-Ran three tanks with seafoam when I first purchased the bike
-Stock exhaust had holes drilled through the baffle next to the main outlet (I can provide picture if necessary)
-Starts instantly and gets decent mileage, ranging from 36-40mpg
-TPS mod done (500 ohms with throttle closed and 4,000 ohms at WOT)

 

Symptom 1 - carb fart - perfectly normal just make sure your idle speed is set to at least 1,200rpm so it doesn't inadvertently stall.

Symptom 2 - Check your vacuum hose and the petcock rubber diaphragm for splits.

 

If you have done any messing about with the carbs (cleaning, removing, changing jets, etc) you'll definitely want to sync them afterward. You don't mention this, and it will make a difference in how smoothly they will run. It will definitely help with carb farts as well.

A more tedious but perhaps more helpful item of action would be to look at 8541Hawk's carb setup thread. Often size 48 pilots will make these bikes run better on a stock motor (other experienced members disagree and think that the stock 45's are ideal). I find I like 48's better with my bike (and pulling the choke indicates that this may help yours). You may also want to make sure your slide diaphragms are functioning along with the petcock as Wicky said.

FWIW I have nearly zero carb farts (every once in awhile at 3500rmp, but not on a regular basis).

 

Thanks for the replies. If I have time this weekend I'll work on the bike again.

I took off the petcock when cleaning the carbs to inspect it. If I remember right the diaphragm portion of the petcock cannot be opened easily. Is that right? Everything else looked perfectly clean and new from the petcock on down. Speaking of the petcock, what’s the purpose of the small outlet nipple on the underside of it? No hose was attached to it. Probably there as a breather to allow a pressure differential between atmospheric pressure and the carb pressure to open up the diaphragm?

Is the rear slide supposed to be harder to open than the front slide? There's definitely a difference between the two carburetors. I figured it was supposed to open slower to keep a richer mixture for the rear cylinder bank (keep it running cooler) but I'm probably making that up. Now that I’ve looked up the part numbers the springs are exactly the same front and rear as are the slides. What could be making the slide move slower? Maybe there’s not enough vacuum on the diaphragm to overcome the stickiness to open up the rear jet needle until about 6,500 RPM (throttle at least ½ open, ¼ open doesn’t overcome the ailment)?

Could it somehow be the regulator/rectifier?
I did not sink the carbs because I was on a time limit doing this work. I have the necessary tools so I’ll sync them and see if that helps with the carb farts. I’ll also open up the carbs again and check what size jets I’m running. There’s blue paint that looks to be used for alignment on the head of the pilot jet and it looks like a dremel was used to make a notch on top for a flat head screwdriver. I figure you’d only need to do that on a stock set so for now I’ll assume there #45’s.

How would putting #48’s work better if that makes it run richer? Wouldn’t that dump more fuel and cause even more backfiring? Just curious. I’d rather run richer than leaner though so it’s worth a shot.

Thanks again for the input.

 

Yes, this is not easily accessible. It should not leak when the motor is off. The messy way of testing it's functionality is to suck on the vacuum hose attached to the back. If fuel starts dumping out, it's working...

Exactly. It's also a decoy in which many a person has attached the vacuum line to it and had poor performance as a result

Definitely not. This is probably your problem. The front slide probably has a hole in the diaphragm or is not seated properly. The resistance is from air pressure that a diaphragm is holding, and if there's a leak it is very easy to open. They should also close at the same speed when you let go of them. This would explain the huge hesitation in the mid range as the air pressure is not correct for the slide to function properly until enough vacuum at high rpm's cause them to open properly and perform as normal...


Doubt it in this case. The symptoms don't seem to line up to electrical, IMO

It wouldn't fix the second problem but it does often solve the issues you're having between 2500 and 3000 rpm... due to EPA and such these bikes kind of run lean. It's also worth noting that in other countries after '99 these bikes came with 48 pilots stock.

Edit: changed my mind about what the slides were doing in the mid range They need a little more diagnosis, but are definitely not working correctly.

 

Thanks 7moore7 and Wicky. Problem solved. The TPS was definitely not being activated so when that was fixed I had power above 6000 RPM. Putting the carbs back together is what caused the mid rpm issue. The diaphragm was indeed the problem. When putting the diaphragm cover back on one of the carbs the diaphragm was not seated correctly which made it difficult to open up when a vacuum was applied. Took me 30 minutes to fix, took it for a spin, and bingo, the bike has power. I'm impressed by the smooth, linear power these bikes produce. It's very predictable. Thanks for the input!