communication problems?

Hey everyone. I work at a shop and were just buttoning up a 65 Mustang fastback with a Edelbrock supercharged gen 2 coyote with a ford PCM and the ford control pack. They told us that it was dynoed and tuned with HP Tuners. Ever since we got it fired up, its been throwing all sorts of cam codes. P0340, P0344, P0345, P0349. Talked to Ford Performance and Edelbrock and got a few different diagnostic charts, did all the procedures, and still no change whatsoever. We had a tuner swing by, who uses HPT a lot, and his laptop wouldn't communicate with the PCM. Have any of you had this issue before? We've used several different scanners just to retrieve the codes, but the tuners laptop and another generic Bosch OBD2 scanner will not talk to the PCM. ANY help would be great. Thanks a lot!