Max,
I'm very proud of my "rack" hehehehe. I'll try to explain how I countersunk the top nuts.
On the top shelf I did not use washers. I drilled about 1/2" down with a one inch drill bit, then the rest of the way with a 5/8" bit. Rather than use the standard 5/8" #11 plain old nuts on the top, I used the locking type (with a nylon insert). I tightened them til they locked, then used the nut underneath the top shelf (that does have a washer) to crank it and pull the locking nut into the 1" recessed hole. Hope this explanation makes sense...