Whether or not you've purchased anything from them, give DTT a call. The folks there are excellent at customer service . . . even if you're not a customer you may end up being one . . . and they treat everyone the same. They don't have any problem answering questions over the phone. I'm not sure where you are in the country, I'm in Eastern PA and had my trans DTT'ed a few years back at TRD Diesel Performance (Tim from VA Beach) if you are in his range I'd be happy to share his phone number with you - PM me. Otherwise call Bill or Stephan Kondalay their site
Diesel Transmission Technology - DTT Performance Diesel Transmission and Power Accessories very helpfull. When I was having problems with my trans @ 139 k (stock no pref bombs) I had already decided to go DTT when the time came. To reasure my decision, before the big purchase, I called and they helped me troubleshoot over the phone. Of course when you have ton of band material in your pan (as I did) it was a good guess the trans was toasted.
In a guess, to me, it sounds like you've got some "control" issues or something not communicating correctly. Give the folks @ DTT a call. Have you tried to reprogram your APPS? Disconnect batteries for at least a half hour, reconnect, turn key to "on" position (don't start), "very slowly" depress go pedal to floor, and "very slowly" release to top of travel. Turn key off, then start as usual. This helped me (for a while) with the OD in/out hunting due to interference with electrical noise from alternator - then I got the DTT noise eliminator (for like $30). This was before rebuild and it worked so well it helped my decision to go DTT, it's still on 20k miles after rebuild. You never know the reprogram may help.
Another idea, it could be the cable to the APPS has stretched ? ? ? I know I had a heck of a time getting mine set right (Tim from VA actually played with it for over an hour to get it to shift where I wanted it to). Now that I think about it, it if this cable isn't set right it screws with the entire shift point issue - sounds like you may have an adjustment issue. Be carefull with the littl white clip that locks the barbed adjustment on the cable as if you break it you have to buy a whole new cable and start from scratch - and from what I've heard here those cables are like $400 +/- so you may want to connect up with someone local to you that's had to screw with these cable adjustments.
Hope this helps somewhat - before doing anything though give the folks at DTT a call and let them give you a few more ideas - sounds like an adjustment to me - in a knee jerk reaction - after think about it a while - sorry for long reply but hope it helps somewhat. I know if you have a "work" truck that's not "working" not only does it cost $$$ but you ain't making any to boot. Give DTT a call.
Best regards, Joe Mc