Although I left enough space for the epoxy to form a meniscus at the edges, I decided I wanted to get the rails right up to the edges, per the original design. I used a shoulder plane while the epoxy was only partially hardened and it planed down beautifully to remove the meniscus along the outer edges. After the leveling epoxy was completely cured I bonded the aluminum rail mounts (with rails still installed) into place on the gantry, using an adhesive epoxy. I think I forgot to mention earlier during the Z Axis buildup, that all the aluminum bar stock was chemically etched prior to epoxying them to the plywood, in order to get the best bond. On one set of rails, I sanded the bonding surface with 120 grit prior to etching; another recommended method for better bonds. I’ll see how each method holds up and perhaps do some more formal testing of different bonding methods in the future.
To help align the rails, I placed identical length aluminum bar stock in between the rails at each end, where the ball screw supports will be mounted. Then I built part of the Y carriage and installed it on the rails, to hold them in alignment at the center.
Once the epoxy cured I put a dial indicator on one set of guide bearings and measured the error all along the length of the opposite rail. I loosened one to three rail mount screws at a time and made fine adjustments to the rail until I had no more than +/- 0.0005” error throughout the full length.