dilema

[Mondo]

I recently had a 2008 5.3 installed in my 67 (never mind the engine cover). The original computer had some pins bent and looked a little rough (junk yard hacks).
So I bought a new one (also needed new trans module). Took it to the tuner and it runs good (300hp at wheels). But it has an error because the crankshaft sensor is not calibrated.
The tuner said he couldn't do it and to take it to a dealer. The dealer said he couldn't get it to learn due to errors etc.. Went back to tuner and he still believes they can "force" it to learn. And perhaps that dealership guy doesn't know that.
Any ideas?
Furthermore, I straightened the pins on my original computer, we hooked it up and downloaded tune. No problem with crankshaft sensor but I have a high idle situation. Read it might have to relearn and can take 150-200 miles. On both ECUs, the transmission shifts hard from 1st to 2nd.
Any recommendations (not a lot of tuners around here).