First we are talking about a 79 F250 4x4 with a 7.3 IDI swap..It has a E4OD behind it .

1st to 2nd is fine, then huge rpms before it hits 3rd... Way above what a diesel should be....I've taken it back to the transmission place twice and even taken it to a second transmission place...
They proved it wasn't the transmission itself ( $1700 rebuild) when they hooked it up to a box that controlled the pressure in the trans. They said when its reading wrong it will throw up high pressures and the trans will drive like mine has with really hard shifts etc... This box was hooked up to my trans and the mechanic operated it from the passenger side while I drove...it shifted like a dream....then he showed me different pressures as he adjusted it from the box...and I could definitely tell the difference...
They said they didn't know if it was the wiring or one of a dozen different sensors...

Where should I start looking? Transmission shops are both saying they can't read but a few codes because of the swap and all codes are good to go now...the ones they can read anyhow... I know this issue is a limp mode of sorts....but anything I can look at before I just put a diesel c6 back in it?

 

You can try to get the codes yourself. Without codes all I can tell you is that it isn't right.

Ford ? OBD Trouble Codes

 

so it has never worked right, or it just started to do this? there are three sensors that are important and codes will help determine what sensor is out of spec..if you still have a lighted over drive button that comes on and goes off when you put it in and out of over drive if this is flashing its in limp mode.