I'm not sure your test of flatness on the x-axis bars is valid because the rails weren't bolted down. If there's a dip in the bar the rail will probably span it but get pulled into it (slightly) when bolted firmly down. I think you'd need a long straight edge and feeler gauges to really figure out if it was flat enough.

As for cutting aluminium my SCMS went though that 10mm you gave me like it wasn't there using a positive rake cross cutting blade - about the worst blade you could use for metal cutting - and left a mirror finish. With a negative rake aluminium blade I'm sure you could do 20mm easily. Watch out for those chips though, as Jazz says, they are bloody hot. As for routing to shape you might want to try a router table instead of a free hand, I think you'd probably get better control over the depth of cut and a finished face this is more perpendicular. The downside of of a router table is that the chips will fall onto and potentially into the router which may not end well. You can pick up a router table insert for very little as long as you don't mind the height adjustment being completely manual.