Does anyone modify them by shortening the trigger rod? I read about it in an old magazine but don't know anyone that does it or why? Does it help to wax them or treat them with trap dip? Any tricks to setting them?

I never actually cut the trigger rods, but I did used to bend them a bit, which did shorten them by a hair. This would make the trap more sensitive. And I used to spray them with a aerosol based grease to try to slow down the rust.

Do you put clothes pins on the stake to hold the loop on the trap in the right spot? Do you cover the hole at all with grass or leave it open? I usally cover with some dead grass.

I never used clothes pins, but sounds like a good idea, and I have heard that before. Yes, I do cover the tunnel opening after placing the traps, usually with a wad of grass or a dirt clod, then put some more dirt over that. But I know it also works great with leaving the tunnels open after placing traps.