OK. I've been studying this since it happened. I have heard a lot of theories. But only one is a clean novel theory. In fact, this is only theory that fits every fact of the story including the reference you made to the discrepancy in bullets.

Paraphrasing an old theory, the correct answer is often the simplest. I will just state the bottom line of that theory here without going into the supporting evidence which is voluminous. Oswald did hit Kennedy, but in the neck only. It wasn’t fatal. The fatal shot was from the Secret Serviceman’s rifle in the car behind Kennedy. That’s how the bullet tore his head apart. It wasn’t intentional. It was a mistake. The agent was standing up and when the cars accelerated after Oswalds shot, he fell back and discharged a round freakishly into the back of Kennedy’s head.

I recently watched a show about the Kennedy assassination and while I'm not a big conspiracy buff, a couple of things bother me. (1.) They found 3 shell casings on the floor and assume he fired 3 times. (2 casings fairly close together and 1 some distance away) Does this mean he fired 3 times? Not necessarily. There could have been a shell casing in the rifle from the last time he fired it prior to November 22. This could explain why one casing was some distance from the other 2. I would like to know what was in the chamber when they found the rifle. (A) a spent round casing (unlikely) (B) another live round (C) nothing (2.) The bullet that struck Kennedy and Connelly (the single bullet theory) went through Kennedy's back and neck, broke a rib in Connelly, shattered Connelly's wrist bone, and went into Connelly's leg was largely intact when it fell out of Connelly's leg onto a gurney at the hospital. It is only slightly deformed. The bullet that hit Kennedy in the head literally exploded on impact. (You can even see the explosion on the Zapruder film) Witnesses who were present at the autopsy say the x-rays showed numerous small fragments in Kennedy's brain. These are clearly 2 different types of bullets. Would Oswald, who was somewhat of a cheapskate and perpetually short of money, have purchased 2 different types of ammunition? And even if he had, why would you load different types of ammo into a magazine?