I think where some of the confusion comes in is that (as I recall) Shepard's Mercury spacecraft (the capsule) was production #7. The *mission* designation however was MR-3.
Because it was production spacecraft #7, Shepard chose the name "Freedom 7" as his official *spcaecraft* name.
However (yep, it gets a little more confusing), because there were seven Mercury astronauts, when Gus flew the next mission (as a gesture of teamwork and fraternity), he kept the "7" designation in the naming of his capsule, calling it, as we all remember, "Liberty Bell 7", even though it had to be, one would assume, spacecraft #8 to come off the assembly line.
And so, each following Mercury astronaut used the number 7 in the naming of their *spacecraft*, though Shepard's was actually the only one that really was capsule #7.
The *mission* designations however did run MR-3, MR-4, then the MA series missions for the Mercury-Atlas orbital flights.
I think I got that right....
Earl