Just throwing more ideas out:
Do you know if the shift kit was installed 100% correctly?
How long did it remain in running condition after the kit was installed?
Do you remember it doing anything funny before the motor problems?
All fluids if left to sit over time lose their ability to function like they should. They begin to collect and cause buildup. You might need to have the tranny flushed, instead of just new fluid.
If it's not a solenoid or TPS, it's going to be something internal. A stuck or sluggish valve etc. If you've seen the inside of an auto tranny it's hard to believe they work as well as they do. It's just sounds to me like it's taking the transmission an extrememly long period of time to build up the needed pressure to shift, or it could even be a failing clutch pack.
My personal opinion, I think it's going to be a band, clutch pack, or something else mechanical relating to that gear only being that the rest of the gears seem to work fine...assuming the shift kit was installed correctly.