About a year ago I had the same trouble. At Sun 'N Fun I set out to view and photograph as many tip-ups as I could to see how common this issues was. Out of 23 tip-ups, 22 had visible issues at the same 10 and 2 positions. Only one guy managed to get his perfectly smooth. When I asked him how he did it he said it took him quite some time - and he did it with shims.
That's how I did mine, and it does work. After you make sure there is zero interference with the left and right aft sub panel flanges, the center seal strip and the frame wasn't drilled with a 'sag' at the center splice plate - mark on the frame skin where the it bulges. Then make shims to go under the forward top skin in the marked locations. Be sure to taper the ends of the shim for a smooth transition, and start with .032 shims. Match drill to the sub panel forward flanges.
I would wait to do this shimming after you have completed the canopy, since it will be the forward skin you will make match your frame skin - and the top forward skin will be one of the last installed. Plus, as you add the struts and the canopy forward fairing, the frame will stiffen up significantly. The bulges won't necessarily go away, but they may change somewhat.