That's great you have the machine working well, despite the lack of build quality I still think they represent great value. One thing I did with mine was to jog to the very extremities manually and before the limit would trigger, and then manually cut a fine line while jogging it to create the largest possible rectangle it could do, I then used this to as accurately determine the error in psotioning and accuracy. From memory I had to adjust the steps per pulse slightly to get the highest degree of accuracy.
I'm curious to see how you go with the limits for positioning, I thought they aren't very repeatable to any high degree of accuracy given they inductively pick up the "nearness" of the metal? If your using Mach3, you might want to have a look at the interfaces from Ger21 or hossmachine for auto-zero functionality. I'll eventually convert mine from NCStudio to mach3 for exactly that reason.
cheers,
Ian
It's rumoured that everytime someone buys a TB6560 based board, an engineer cries!