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I just recently got a tune update from a popular tuner and when I was driving in the normal mode tranny shifts seemed a little harsh.. So I used the tow/haul mode to soften the shifts and it's did except when slowing down and decelerating the tranny seems to get mixed up and downshifts very slowly waiting eventually causing a hard 4-3 downshift. This was present even when braking normally, as you let go of the gas the normally a vehicle kind naturally slows down, the tune seemed to keep the truck from slowing down via "engine braking" or coasting down the gears? Anyone else have this problem with a tune?
 

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That doesn't surprise me, as both the tranny and engine are controlled by the PCM and it's programming. Many of the canned tunes play with the shifting firmness.

I haven't had an after-market "tune" on this vehicle yet (on other vehicles yes), but I had a PCM update from Ford in August (for Emissions & Fuel Economy). My PCM "learning" was cleared, and it seemed to shift a bit "funny" at when I first started to drive it (but I expected this). But after some driving with varying loads, speeds and rpms ... the transmission shifts beautifully now.

Give it a little time to "learn" and see if it smoothens out. If after a couple of weeks it still shifts harshly, contact the tuner.

PS: Which tuner did you use?
 

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Take into account that the PCM also has adaptive settings, the first few days you may experience harsh shifting as the PCM adapts it's shift habits to your driving style. When tuned the tow mode switch helps soften the shifts, however, it also still performs as tow mode should, holds gears during decel to help slow the vehicle down through compression braking. The tune I use under heavy accel damn near snaps your neck when it hits 2nd gear, I prefer the firmer shift, it's actually better for the clutchs, the soft shifts are achieved by slipping the clutches under a continuous pressure increase until the gear fully engages.
 
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