Ask the <expletive> customer whether they need a push fit or a clearance fit. Warn them they may have to ream the holes if they need a push fit. For a clearance fit, 3.5mm and 5.5mm should do nicely as typically good quality LEDs have a diameter tolerance of 1 thou, (0.25mm). If your mill or drill press has a bit of runout and tends to drill oversize, you may need to go down to 3.2mm for the 3mm LEDs