The numbers refer to the 'release' model of the bike, a bit like software. I think it goes something like this;
The letter refers to the 'major' model, 'A' being the very first one. The numbers refer to the 'tweaked' models. I.e., when a major overhaul of the model comes along (when the bike changes dramatically), the letter changes, when it's just tweaked a bit, the number changes.
So, the higher the letter, the newer the model. I think we're one J2 now aren't we?
I stress that I am not sure, this is just what I think.

The Man in Pink
T'was Mr. Dazzle, he
IS the Mr. T of us lot.
- Irn Bru Freak