Short of printing new brackets, you can countersink the wood ones to use bolts and nuts as well. One might be able to drill the switch holes out to take larger hardware, but the holes in the switches are sized for M2.5 hardware. A 3/16-inch bit works to countersink the M2.5 bolt head so that the bracket will sit flush on the rails. More info and a picture of this is in the ENDSTOP INSTALLATION post in my build thread.

You should also make sure the bolt used to mount the bracket to the rail isn't a bit too long. The M5 screws that came in my kit would start to bottom out in the v-rail channel as they tightened. I filed just a bit off the threaded end in order to make sure the screws properly clamped things like these brackets to the rails. I didn't really remove much material - just cleaned up the ends of the bolts.