1) Im using 1/2" aluminum, generally its probably flat enough for no critical parts, but I would consider getting your aluminum from Misumi, they do 6 side machining on the plates for a reasonable price.
2) Im bolting the SBR20 supported rails directly to the Misumi 6 series extrusion. While the extrusion may not be perfectly flat, its probably good enough for most uses and the SBR rails can handle slight misalignment better than the Linear rail type which are much more rigid.
3)Many professional systems use belt to connect the motor to either the screw or pinion. They work well, you should have no issues if you plan it well and allow for adjustment and proper tensioning of the belt.
Im using AT5 belts and pulleys, also from misumi, they seems very well suited for this type of application.