Hey HondaMan thank you for your help! I tried without the air filter and it was different. Idled fine and throttle responce was good too. During the ride it had a different surge or stumble at the same RPM but took more throttle so I have a Brand new aftermarket air filter so I installed it. It seemed to help but didn't cure it! I'm thinking it may be rich also. Like I said before I'm not sure if it has Honda Needles or not so I may try moving the clip to the 3rd position and give it a try. By the way the Dynatek Ignition does use the stock Honda Mechanical Spark Advance. I also have some K & L carb kits that have the stock size jets and needles should I try them?
In my experience, the K&L (and Keyster) needles run somewhat leaner than the Keihin needles, and also require the associated K&L (or Keyster) emulsifier tube be used because they are bigger ID hole diameter than the Keihin. That can make the K&L/Keyster needles get stuck (or at least a tight fit) into the Keihin needle jets when the throttle is released: when you have it apart, look for a 'polished' spot on those needles nearest the slide itself, to see if they might be getting 'stuck' into Keihin needle jets from below.
All that said: I've generally found the K&L and Keyster parts tend to run leaner than the Keihin parts, which usually affects throttle response where the engine is moving off the pilot jets and into the slide-and-needle jetting. It's not that they don't work: they just need to be experimented with to get them to run right. This most often gets mis-started (in carbs that have been sent to me for "repair" from this) when someone installs the K&L/Keyster needles, but leaves the needle jets as Keihin's own, so the hole is too small. More than once it has been the other way around when someone had the K&L/Keyster needle jet in the lower part, but the Keihin needle in the slide: then it runs too rich because the needle jet doesn't get fully shut off (and metered too richly) by the thinner Keihin needle.
So, try to make sure both the needles and the needle jets are at least the same brand!
Then: if you use the Keyster/K&L parts, anticipate that it will run about 7% lean or so. For reference: each notch in the needle on the 500/550 slide is a little over 1% difference in richness/lean-ness, and K&L/Keyster jet numbers are also about 7% higher for the same value: for example, a #100 Keyster/K&L jet feeds like a #93 Keihin. Thus, having a #98 (typical of many 550 setups) Keihin mainjet converted to K&L/Keyster means the new one will be #105, to the closest number, for the same fuel feed.
While I don't know why Keyster/K&L changed their needle thicknesses and needlejet hole sizes, I have learned that the number differences in jet size comes from having different taper angles inside the jets, based on carving apart some of each some time ago (just to look). This means the flow characteristics are just a little different between the jets. It might be a patent-avoidance thing? Mikuni is similar.