I completely understand what you are talking about with the shifting... a few years ago I tried experimenting with doing half a build on a trans. I did all the pressure mods (Mike L springs, Transgo shift kit) and then put an Upgrade C3 Alto kit in it, piston/steels/frictions. The kit had one more friction and steel over stock. Didn't have the money at the time to do a full build, and I had smoked the stock trans, did the "build" on a spare trans I had lying around). That half built trans as I called it, did the same thing with funny shifts, so I ended up pulling it back out. checked the clearances on the clutches and they had compressed a fair amount... well out of tolerance. So I guess what I'm saying is your clutches could've compressed or worn down a bit over time and the TCM is slow at learning the "updated" tolerances. I know my truck acts different in 4Hi going down the strip than it does in 2Hi on the streets. Does it feel like it bangs into any gear, ie a tie up? (just trying to think of what could cause a slow shift without changing the tuning)
The tires I raced on for those time slips were a snow tire of all things (sticky, soft rubber). They are 285/65/16 on the pyo's at 35 psi if I am remembering correctly. I am running traction bars that I built (T&B fab style/ Chevy1925 on here), bilstein 5100 shocks and I have the overloads pulled. I'm pretty sure my truck doesn't squat to bad. You are definitely loosing a bit because of energy that goes into squatting the truck. What kind of traction bars are you using, how do they mount to the axle?