Hmmm, anything else change besides the exhaust?

If you just changed the exhaust then it could be a physical transmission issue. I would change the shift settings of the shifts to make sure the upshift and downshifts dont overlap. Also, I noticed your mph shift points are waay off, I barely got to 42-43mph at 6100rpms and 3.73 gears. No reason yours should be set to 46mph with your 4.10s. Change them down to like 40mph and smooth the shift points as well, I keep my mph set to 40 then use the RPM point to command the shifts at WOT.