I know for a fact that the jetting recomendations in the dynojet kit are very rich. When I installed mine it called for a DJ175 MJ and I finally ended up with a DJ150 MJ. Also, I had to drop the needle one notch from what they recommended. It did exactly what you are describing till I lowered the MJ. It would stumble hard till I lowered the needle. I would check everything over, but I bet that is the prob.
2001 416EX with Sparks X-6, FCR 39mm, ELKA Triple rates with cans, Burgard +3+1 A-Arms, Elka Linkage with Custom Axis Rear shock, Denton Steering Stabilizer, WISECO 87mm 11:1 with Hotcams Stage II, FDO Heavy Duty Head Studs, WB Rev Box, K&N Air Filter, Cascade Parking Brake Blockoff, AC racing Pro Peg nerfs, Renthal Sprockets, Renthal bars, DG bumper, DG Swing arm Skid, RPM 2+2 axle, speed locknut, Magura Jack Hydraulic Clutch
1988 TRX350R ported by NRPD, ESR TRX5, PWK 38mm A/S, Gibson Long Travel A-Arms, Elka Quad Rate longtravels, Laeger Swinger, ESR reed block
2007 CBR1000RR, Akrapovic Full Race, Comp Werks FE, DynoJet PCIII, ShoGun Sliders