96 Dakota 4wd 318. 256k. Trans rebuild when I bought it at 170k with said trans in bed of the truck. Stock rebuild, plus a TF -ODjr shift kit. Ice owned 8-9 years since then.

Has been great til earlier this year when the return spring fell off on the KD linkage at trans
Fixed that and was good again. Seemed like I remember it acted differently when that happened though.
Til about 1000 miles ago. Doesn't slip, all gears there and lock up as well.
Problem is shift timing. And not all the time. Sometimes shifts great, sometimes 1-2 will NOT happen until 3200 rpm no matter how easy I am on the gas pedal. 2-3 similar, at or slightly below 3k when it's acting up. Then short shifts into 4th. When it shifts like that 3-4 seems normal. When it shifts as it always has before this started, then 3-4 is a little harsh. No rhyme or reason for when it will shift normal or when it will shift stupid. It can shift several times normally then stupid once and back to normal, or it can shift stupid several times in a row and shift normal once or twice then back to stupid. No pattern as to when it will decide to do what.
This truck is not long for this world, has been demoted to winter beater with a heater the past couple of years. To keep miles and salt off my 2wd 1/2 ton in salt season.

So, you have roughly 80,000 miles on the trans now, have you changed the fluid since the original install?
I believe I would start with resetting the kick down cable, probably won't help, but its pretty easy and may help with the problem. Could be an issue with the cable & linkage not moving like its suppose to, since its mostly driven in the salt & slop now.

I have a 96 Dakota 5.2, 4x4 stuff in my 49 that originally had 44,000 miles on it (now has 63,000 miles on it). When I use the truck, I back it out of my driveway, then shift it into forward to drive away. I have found that it doesn't like to go from reverse into drive and pull away as soon as it grabs. Almost every time I do a fast direction change and want to drive as soon as it grabs, it messes up the shifting. It wants to hang in 2nd a lot longer then normal. If I pull over, put it in park, shut it off, then restart it and put it into drive and wait a couple seconds before moving, it shifts well.

I have read that the speed sensor at the tail end of the trans determines the up shift rpm. I don't believe Mopar units are available any longer, so maybe when the aftermarket speed sensors get older, they don't function so well. There is also a relay in the under hood fuse box that controls the OD and the solenoid pack in the trans (mine was labeled on the box cover as a fan relay instead of a trans relay, the only thing that used an electric fan was the 4 cylinder, that is an early production 96 deal). Maybe that relay has some corrosion on its terminals.

As said above, that tailshaft output speed sensor sounds like the culprit to me. I have an '01, and that sensor got broken off while I was driving through brush. Acted just like that. They're about $20 and easy to change out.
Check the wiring too though.

Is this actually an RE trans or an RH trans?

Having throttle valve linkage and being a 96 indicates RH.

Very different diagnostic procedures for them.

Speedometer working? The pcm needs to know the speed when/how to control the trans. As mentioned was the TV cable adjusted? Where all the electronics in the trans replaced? Are you getting any codes?