The RFS MXC models were delivered later so perhaps that is why there are still some left. Earlier in the year I had no problem locating new EXC thumpers but there were no MXCs to be found. New for '01 the MXC is obviously the rarer version.
First gear is about 18% lower in the EXC, second 9%, sixth is 6% taller. That is a significant difference IMO and easily noticed. The 520 SX shares the first four gears with the MXC, so for moto I guess the MXC, harescrambles/enduros the EXC. In really tight stuff you may not like the taller first gear of the MXC.
Since the tank and light can be easily swapped I'd say the tranny is the deciding factor, although parts swapping on a KTM is never cheap...
The only difference between the 520 and 400 is the displacement, the bigger motor is very fast but IMO the power is easy to manage. The 400 is like a big, fast (but light) electric motor. Either one is the easiest to ride yet still fast bike I've ever been on (but I currently ride a 426).
If you get the 400 you will have to put up with a bunch of loud blue thumpers getting the holeshot at the track, but the 520 is too fast for that.