1982 Yamaha xj550 hesitating with carb mods?

So I had the airbox removed and the carbs fitted with K&N pod air intake filters. The jets were moved up 2 sizes from 1.12 to 1.25 and the carbs were tuned to suit. I have not done any exhaust modifications yet but am planning on buying the Mac 4 into 1 complete system. I am not experienced enough to do this kind of carb work so had a very well known and trusted shop do the job for me. The exhaust is my next thing and will have the shop do that as well since the carbs might have to be rejetted again.
Now, I do feel a huge difference. Plus they look cool and the bike sounds so much better. But now I get hesitation. If I give it throttle while riding or when taking off it will hesitate for a sec then perform phenominally. It feels like my powerband has gone up a little into the higher rpms but its performance is insane. I can get to 70+ in second gear in no time.

The hesitation is the only thing that bothers me. Is it because of the jet and intake mods with a stock exhaust? Or is it not getting enough vacuum to get fuel into the carbs? Was also wondering if my petcock might actually need to be modified or does that not matter?

well... any insight would be much appreciated. And Jance... I expect to hear from you:)
 
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