Minicocker is just another Cocker...
Ok, perhaps I should explain this to you: a MiniCocker is basically identical to a Cocker except in a few part size aspects. The only material differences exist in the vert ASA being on the front block instead of behind it and existing as a different part, the pump rod and actuator (timing rod, connects to the 3 way) rods being shorter, and the chamber in front of the valve being significantly shorter. All other parts are identical and function exactly the same way.
How does this effect you as the shooter? Well, because the Mini is shorter it balances differently, which only by picking one up and shooting it can you see if it's right or wrong for you. As with any gun, the single superceding factor in selecting your gun of choice is that it fit you as the shooter to be able to use with maximum effectiveness (accuracy, pointability, low to no chops, speed, maneuverability, etc.). Also because the valve chamber is shorter it has to be bored out more and/or accessorized with a low pressure chamber in front to be able to run as low pressures as you could get from a Cocker of similar specifications with the same valve and springing.
As to your first question, 99 or 2000, I'd go with the 99 because most aftermarket Cocker parts are for pre-2000 Cockers and 2000+ aren't always as readily available in all places yet. Plus you can probably get the 99 at a discount since it's not the current model.