The differences (Apart from milling) between a 98-99 cocker and a 2000+ cocker are:
Bolt length, 2000 bolts are shorter than 98/99's (And longer than 99 STO bolts). The bolts are interchangeable as long as you also swap back-blocks (2K bolt requires 2K back block and vice versa).
valve chamber size, 2K's have a larger valve chamber and are better for building LP guns(Especially for mini's, which were effectively HP only until 2001, there were no 2K minicockers). Valves themselves are compatible between 2K and 98/99 cockers, as are all internals
Banjo bolt/front block. The 2K has a much larger diameter banjo bolt (Legacy of the valve chamber size), so front blocks and banjo bolts are not interchangeable between 2k and 99 and earlier bodies.
Trigger plate and gripframe. 2k and later cockers have an STO trigger plate, 2K VF and 2K1 and later cockers also have the STO 45 frame. All cockers from 98 on use compatible frames and trigger plates, 97 and earlier cockers use incompatible frames and trigger plates (interchangeable as a unit, but 98 stule trigger paltes do not work in 97 style frames, and vice versa)
Note that this applies only between 98/99 cockers and 2K and later ones, 97 and earlier cokcers are mostly the same as 98/99's, but may have some differences (Trigger frames, plates changed between 97 and 98 as well as the velocity adjuster), 99 STO's have some minor differences from 99 cockers(P-Block and shorty bolt,a s well as 45 frame and VF, and milling of course).
Pneumatics have steadily improved, but continue to be compatible accross the entire product line, barrels (except for STO/Outkast/Orracle/BM) continue to degrade.
2k2 VF Cocker, STO/Eclipse Blade, Old-Style 14" Boomstick,
68AutoMag Classic Feed CF11023, Ring trigger.