Get a jet kit...
My quad was doing that exact thing, when I installed my K&N filter and FMF full exhuast. When I would hit full throttle while it was idling, it just put-putted then eventually kick in at high rpm. I first adjusted the air/fuel screw, it helped alittle, but it still had a stalled reaction time. I got the jet kit and tried out different ones until I got the best throttle response. I would suggest that you get one of the kits that come with different jettings. For each engine mod you do, you may need to change the jetting again...I'm running a 150, I think the stock is 145? The kit suggested a 160 with my set up, but I tried that first and my quad still had delayed reation but was very aggressive once I got pass the low end. I then changed it again to the 150 and the response time was great. The kit has a 155 jet as well, but since it seems to be running good at both ends, I don't want to take it apart to find out 155 not better.
Hope you fix the PutPut problem.