Yes, get a vertical drill jig, get everything trued up and using a couple of classic "C" clamp, run a pilot drill through and work up to the finish as mentioned earlier, Do not use rubber faced squeeze clamps, they can move. Each dowel size has it's own recommended final drill size which may or may not be perfect for the wood you are working with. My drill jig has inserts so I clamp the jig up and drill a pilot, switch bushing then a mid size, switch bushings, then the final.
Drill and install one brass square dowel at a time. Drilling all holes at one time is begging for a misfit.
