I finally had time to fill up the transmission with fluid, check for leaks and adjust the ATF level.
Taking it on a test drive I quickly learned that the 2-3 flare is still present with little to no change from before the valve body job. Manual shifting was smooth.
The next step was to read the FSM in
more detail. I stumbled across something in the electrical and transmission manuals that I did not see before. I missed it because there was an earlier fully hydraulic A442F that most references discuss.
The A442F (electronically controlled) has a transmission control module with part number 89530-60170. One of the inputs for this module is the throttle position sensor (TPS). I followed the FSM for testing it and found that it was not correctly adjusted. Way off. Looks like someone had it off at some point and did not follow the FSM for installation. Once I adjusted it to spec and test drove the problem was gone. No more flare and the transmission runs really well.
For those who have the electronic A442F and are experiencing the shifting flare - check out your TPS setup as it may very well be the culprit.
I have read a few posts that mention a discrepancy in wiring labeling of VC and VA in the transmission manual. These statements are (possibly) confirmed by the 1HZ, 1HD-T, 1HD-FTE Engine FSM RM617E. Page FU-108 and 109 show the following and are assumed to be correct.
Another difference found between the engine and transmission manuals is correct throttle position sensor (TPS) adjustment voltage.
Transmission Manual: 0.96 volts
Engine Manual: 0.6 +/- 0.025 volts
The TPS on my truck looks original and because heat can impact the potentiometer functionality over time - I am going to replace it with new and make more accurate adjustments. New part number 89452-36010
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