If your new frame is an ‘05 and later, it has gussets from the factory. ‘03 and most of ‘04 needed the gusset kits.
As far as the order of swapping frames, not much to it. I would do engine first, run the chain around the front sprocket, then swing arm. The rest really doesn’t matter much. Pay particular attention to routing the cables correctly (not necessarily how yours are, since they may be wrong) to be sure they are long enough.
94mm bbk, +4 stroker, Hot Cams, Vertex piston, FMF Power Bomb header and Power Core can, KW black diamond valves/dual springs, FCR39, K&N, Elka long-travel LT fronts and rear, Houser +3, +3/4 LT A-arms, American Star pro xs chromoly tie rods, Dyna non-programable, Tusk +3 axle.