I'm hoping to play with the 8051 torque management tables found in EEXTRA here sometime soon.
But, before you tune a 4L60E that's got over 40K since a rebuild on it, as a part-time 4L60E builder, I would absolutely drop the pan and put in a new boost valve (TransGo or Sonnax 4L60E-LB-01 (or 02 depending on year), and a TransGo drop-in pressure regulator valve.
I do enough of these that I purchased the Sonnax vacuum test equipment, and the pressure regulator valves are shockingly leaky on every pump I've tested lately. That will cause poor line rise, or worse, line pressure oscillation that manifests as intermittently soft shifts. Or, put a pressure gauge on the trans, and watch the needle swing back and forth under load.
I had one unit that went down from 200 all the way to 100 and back during WOT in first gear. A good 4L60E should stay high and touch 220-230psi sometime during WOT first gear. If it happened to shift while the needle was low, the shift would be soft. Having that inconsistency would drive a tuner crazy.
Once the mechanicals are addressed, tune to your heart's content.
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