its crap that dealers tell you that you can mod w/o a custom map or etc. any mod you do you need to get a controller for it.. these things runsuper lean from factory and they could use a controller from the get go..
I have the same problem and I have come across some threads with other people experiencing the same. All are stock bikes. If I stab the throttle from idle the motor seems to stumble for a second before revving up. If I slowly increase the throttle everything seems to work fine. Some people have added the power commander and that has solved the problem.
Mine still does it even after running it for hours. Once it started getting cold here in the winter mine's started to pop on deceleration in third gear, now that it has warmed up some it doesn’t do it anymore. I might wait and see if the stumble disappears once the temperatures get warmer too. I think my raptor is running to lean for some reason.