99 avalon tranny woes

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I'm having a headache over my sister in law's 99 Avalon.

I replaced the starter the other day, battery was disconnected for 2 hours. (would've been done sooner except neighbor wouldn't go away).
So everything was buttoned up, car starts fine again.
I noticed when the gear was taken from Park to Drive, it is met with a clunk sound, transmission & engine hook up nicely, great power, shifting from 1-2 is ok, shifting is somewhat harsh, not smooth like before 2-3 is less harsh and 3-4 is fine.
Fluid level is fine, and was changed about 8 months ago and is still fresh.

I told my sister in law to give the car a few hours of driving to allow the car computer to relearn the settings and relearn the transmission shifting points (just taking a wild shot).

I'm thinking maybe the transmission mount, but all this happened after I swapped the starter.

Is it possible that a throttle cable could've lost adjustment when I moved the cruise control servo cables out of the way? I never loosened any cables.

maybe TPS sensor?

Personally I kinda like the notchy shiftness, adds some character to the car, but I'm sure it'll be bad later on.

any ideas what could've happened?
 
on that car, you do have to twist the throttle cable assembly out of the way. you might have knocked the engine or trans kickdown cable (if one exists) out of whack.
 
If this problem didn't exist before you disconnected the battery, (verify with SIL) then I'd guess that the adaptive learning has been reset. Driving just a little bit likely won't fix it. It's more likely that she'll have to get it fully up to operating temp (transmission) and (possibly) manually run it through the gears or drive normally through several shift cycles. Full transmission temp wont happen for quite a while btw...
 
Thanks for the tips! from my googling this issue, it sounds like I might have somehow misadjusted the cable. so I have to hope I can put it back where it was!
 
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