What's the prefix?
The YZ125A is a tricked up MX125A. Main differences between the two are the YZ's alloy tank, closer ratio gearbox, no auto-lube, different barrel, and electronic ignition.
I don't know of a 'better' gearbox for them, unless you slap in a whole 125C bottom end. The 250 forks are definitely a huge step foward - 34mm (rather than 30), and more travel.
As a race bike, they're miles behind the Elsinore and the KX. But they're a good honest little bike. Given a few mods, they can have the best motor in the class, and handling that's perfectly acceptable, but the 5-speed box will be a hassle on most tracks.