The "J" in Michael J. Caboose must stand for John. The name of the main character from the above referenced video game.
The other two initials, "M" and "C", also have a connection between the original source, Michael Caboose and John, the character based on Caboose. John is most often referred to not by his given name, but by his military title - Master Chief. Which can be shortened of course to MC.
I realize this is in contradiction to the "trivia" stated on the rvb.wikia page but I think I've made a strong case.