I decided to machine the CRS rails first. To accurately placed the holes, I sprayed the rails with a blue ink dye. Then I set a digital vernier caliper to the measurement I wanted and dragged it along my reference edge to "scribe" a line which I wanted the holes along. Then I did the same for the other side to create an intersection where the hole should be located.
Next I took the rail over to the drill press and drilled pilot holes with a small bit. For the rails, the hole location in the long direction is much less important than the location in the short direction (0.75" or 1.25" depending on which edge you reference). To make the distance to the long side consistent I clamped a plate to the drill press as a jig to push the part up against so I only had to align it in 1 direction each time.
After the pilot holes were drilled, I drilled the holes out to a loose fit clearance hole of 11/32. When I mount the rails to the extrusion they will have some play and I plan to align them using a dial gauge and torque them down into location.