Anyone wonder where Max got her fighting ability? It's not like she could take lessons at the school, and why would Jeb know? And even if Jeb did know, it doesn't really seem like Max can win any fight she ever enters from about 4 years of lessons with someone who wasn't actually a 'sensei', does it?
Chances are they were all brinking on feral up to six years ago when Jeb smuggled them out, and then he took it upon himself to reeducate them. The rest is a composite of TV influences, which explains a lot actually.
I've always thought that Max was just a troublesome case, which was why the dog cages, but that she was still allowed some sort of exercise. C'mon, think of other kinds of lab animals -- they all get some form of physical exercise, even the mice.
Treadmill or wind tunnel tests, perhaps? The maze run is canon, I'd assume there are more physical type tests because that's one of the things they'd study.
With reference to a similar case... the only restrictions going on there with the girl were a really fuckin' strange walk, and that resolved itself in a matter of years.
Max, given four years to recover, would probably be physically pretty normal, but language-wise, delayed.