Possible other ideas would be to color JFKs limo black, rather than the same color as all the other cars. This way you can see at a glance more easily what car is JFKs.
Also, the driver of the Queen Mary gave a quick swerve to the right when Clint Hill jumped off to run to JFK. The driver did this in order to move the front of the car out of Clints way so he could run more directly to JFK. I'm not sure how much he swerved the car as the films do not pick this up. It was only probably a slight swerve in terms of trying to represent it on your animation. Off hand i can't remember the source of this info, but i have come across it.
Changing the colour of the limo is an interesting idea so I tested out some different colours and decided that the red was probably my favourite:

Black didn't really stand out, so I preferred a bolder primary colour.
A swerve of the Queen Mary is possible, so I shall have a look to see if I can find reference to one. As you say it's not a large swerve, perhaps mostly due to the bikes on the right hand side (Chaney and Jackson).
One certainty is that several of the Secret Service agents seemed to get off the car soon after Clint Hill. This is in the testimony and is partially seen in the Nix film as agents on both sides seem to jump off. They all get back on very quickly, but I think this delays the Queen Mary by a second or two as it departs Dealey Plaza.