So where did the 3 shots from the sniper's nest end up?
According to those who were there, JFK reacted to his throat wound on the first shot. According to these people, the first shot occurred:
- after z186 (Betzner), just before z202 (P. Willis),
- as JFK was passing between Linda Willis and the Stemmons sign (z196-205),
- when the VP car had completed the turn (it is still turning at z180),
- just as the VP security car was almost finished the turn onto Elm,
- after Mary Woodward shouted and JFK and Jackie turned in their direction and smiled and waved at them.
So the first shot passed through JFK. We don't know what it hit for sure but the Connallys said it did not hit JBC in the back. This is almost certainly CE399. According to the evidence this occurred after z186 and before z202.
The third shot was the head shot at z313. The remains of that shot are likely the fragments CE567 and CE569 found in the car since, in impacting JFK on a downward trajectory from the SN, there was nothing to deflect the fragments from the bullet upward. Since those fragments add up to less than a full bullet, some of that bullet was not recovered. There were flecks of lead in JFK's head and some lead may have been present in the brain and blood matter ejected in the explosive exit spray.
The second shot occurred after the midpoint between shots 1 and 3 and before JBC falls back onto Nellie. I put it at z271-272 for various reasons based on evidence. This bullet struck JBC in the right armpit and caused him to fall back onto his wife. This was "almost simultaneous" with Greer's first of two rearward turns which has already started by z281 when we first see Greer's head from behind the windshield:

This second bullet through JBC's torso struck the back of his radius, which was in front of his chest at the time. The bullet likely fragmented and deflected away from the point of contact with the radius on an oblique glancing blow driving bone fragments into the forearm/wrist. The bullet fragments then continued in general forward and slightly upward path from JBC's radius.
We know that a fragment did strike the top of the windshield frame and one struck the windshield glass. Greer sensed this impact on the second shot. He described getting "a little concussion of it .... maybe when it hit something" (2 H 118). Tague was struck on the second shot (7 H 555) by a lead fragment that deflected off the curb near where he was standing. We don't know how many other fragments from that second shot left the car.