My carbs have been cleaned thoroughly and the floats/jets/seats are all in good shape. It has Dyno-Jet Stage 1 kit and the air/fuel screws are 2 turns out per the D-J instructions. I have a D&D slip on but I think the air filter is OEM Honda rather than a high flow K&N or other. I just installed new plugs and the fuel system from tank to carbs has been replaced or rebuilt.

I've set the idle per the manual around 1200-1300 RPM but it doesn't idle 100% smoothly at temperature. Plus it pops on hard deceleration which would make me think it's a jetting issue. Altitude I ride in is roughly 1K to 2.5K and the temps are mild.

I would like to sync the carbs and I'm putting together a DIY sync tool. Would a carb sync help with a rough idle or popping? With quads like these I am thinking I may take it to a trusted local mechanic and have him take a look at it. Anybody else dealing with issues like this?

I recently shortened my exhaust can but these symptoms existed before that change.

(Yes, I've looked at the sticky for carb cleaning and other various threads)

 

You said you think the air filter is OEM Honda, so I'm guessing you've definitely at least not found any markings like K&N, UNI, or BMC, right? Even if it's not OEM, if it's an OEM-type paper filter, then you can just treat it as OEM.

What year is your bike? And your kind of close to Cali, is it a CA model?

This definitely sounds like issues with your pilot circuit, but have you ruled out an air leak around the carb boots, and do you have good plugs?
If it is your pilot circuit, which I would suspect, bear in mind that the 2 turns out you were recommended, is just a "starting" or baseline setting, after you have tuned the top-end and mid-range, you would then need to just the pilot screws accordingly, if necessary.

You might just need to experiment with those settings, for example, start with an additional 1/4 turn, or 1/2 turn if it seems way off, on all four carbs, and go again to see if you're moving in the right direction... I can virtually assure you that you don't need to go more turns in, unless you increased the size of the actual pilot jet, like from a 38 to a 40.

Just to give you some reference, a 49 state F2, should start at 2 1/8 turns out, with a stock setup, and a CA model starts at 2 3/4 - more than likely, you just need to start turning those screws out a little more, to get things right... if you do have a hi-flow type filter, rather than a paper type, I would definitely start with 2.5 turns.

Good luck!