When Specter interviews him the first time, Dr. Mac says that the neck wound was an entrance wound. The tracheostomy that was done in the ER, of course, obliterated the wound on the front of the neck, so it is only those who where there, Dr. Mac, Dr. Jones, Dr. Clark, Dr. Perry and others who were in a position to know what the neck wound was like. In particular the autopsy would provide no information. When Specter returns about a month later, he tells Dr. Mac something like "considering that we think JFK was shot from the back, with a round travelling at such and such a speed etc. etc. do you think the wound on the front was consistent with an exit wound?" Dr. Mac replies something to the effect of "with all the assumptions you stated, I guess it could be consistent". With that Specter thanks him and packs up and goes back to DC, mission accomplished. Parkland was and is a very busy trauma center and Dr. Mac would have seen hundreds if not thousands of such wounds and would have known the difference between and exit and entrance wounds, and never would have said it was one or the other if he were not sure.
For my money it's Dr. Mac's word against Arlen Specter's, and knowing Dr. Mac personally and knowing all that Arlen Specter has done since, I'll put my money with Dr. Mac and say that the neck wound was an entrance wound.
Also, if you believe the Warren Commission and the magic bullet theory, you have to believe that this most magical of all bullets, goes through JFK, hits Connolly's wrist, then his thigh, and then magically falls out and is found in pristine condition on a stretcher in the Parkland ER. I have spent many, many nights in the Parkland ER taking care of all sorts of gunshot wounds and I can assure one and all that I have never seen a bullet appear on a stretcher, pristine or otherwise after passing through folks. Things just don't work that way.