Backfire shaking
 

Ok all time for a little help....

I am new so please try to be helpful. Thanks

When riding at approx 45 -60 mph I get this noticeable what seems to be a sputter or backfire sound and the bike shakes a little in a few seconds it goes back to normal and acceleration is fine. Rpms are at 30,000.

Problem #2 when squeezing the clutch to use engine breaking the Honda has shut off on me. It fires right back up but has happened several times.

This bike has had a jet kit put in and recently a new motor. Any thoughts to problems? Maybe airbox, maybe petcock my mech has had the bike in and out of the shop all month working on it.... Thank you all

There's your problems.
OK so I know you meant 3K. Engine must be missing in that RPM range. May due to the jet kit. Have you looked at the plugs? Does it have a K&N filter?
I don't understand the clutch pulled for engine braking. Do you mean engine quits while hard braking with the clutch pulled in?

Jet kit is definitely your culprit, but you will have to provide more info on that to guide you and be sure.

If engine shuts off while pulling the clutch, is another symptom of faulty carbs. Once again, find out what was put in, and the carbs will certainly need a good syncing since the carbs have played with plenty.

I also recommend visiting the knowledge base of this forum, there is plenty of info concerning your issue. Enough for you to read till your eyes bleed.