Start from the larger parts, working on square, then work down to the smaller parts.
For some reason, the instructions for squaring the machine were left out of the XL assembly instructions (but for some reason, these aren't linked from the main site). They are repeated at:
Once the machine is square (or as square as one cares to make it --- there is a point of diminishing returns, and it will run true to itself), then one can determine the belt calibration --- this is best done by cutting small pockets and measuring pairs of them edge-to-edge as noted in:
Once that is dialed in, then one can determine effective endmill diameter (which is actual endmill diameter plus runout x2) --- cut some slots as you noted and calculate the diameter as an average, or cut the diamond-circle-square test as noted at:
(measuring the steps in that will also allow one to dial in the Z-axis)