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How do I decide how to space the drilled holes on the enclosure?

For example, what is a typical distance in between the holes for the knobs, the distance of the footswitch/knobs from the edge of the enclosure, and so forth? What are some standard measurements and layouts of typical pedals such as MXR in one, two, three, and four knob layouts?

Pot spacing depends entirely on the size of the knobs you're planning to use. I don't know if I've ever seen any "standard spacing" listed here or elsewhere, but as a rough guide I tend to drill the footswitch centre hole 18mm from the edge of the box, and the pot holes 15mm or so from the edge.

When I started out, I would make a paper/card net of the box size I was going to use, fold it up and glue it to make a 3D model of the box, and mark potential drill hoiles on in pencil: After eyeing up the clearance, I would actually punch out those holes with a pencil, and mount the pots and switch on the card model to check it would all fit together with no issues.

Position of the footswitch will depend on whether you are going to have an internal battery or not. If I'm doing a 1590B box with a battery, I usually put the hole about 30mm in from the bottom edge. This allows you to sit a battery behind the switch.

I agree with Nocentelli in all his other comments.

As a general rule I always try to keep pots and toggle switches as far away from the footswitch as possible, to prevent them being knocked or even broken by hobnail boots.

Wow, thanks, I am learning a lot quickly on this board.

Another question, somewhat unrelated, is there an advantage to using the white plastic washer on the 3PDT footswitch? In my opinion, it cheapens the look of the pedal and I'd prefer not to use it.

Some guys (me included) like the washer - others hate it.

Your choice.

The reason I like it is that it stops the metal nut from graunching up the finish on your pride-and-joy pedal.

Personally, I don't like the look of the plastic washer. I always replace it with a steel one from the local hardware store.

I just bought some more steel washers, so if you're inclined to use them, here's more info.

The common USS 7/16" washers fit loose around the switch and have an O.D. of 1-1/4".
The washers I like are SAE 7/16". They fit more snug around the footswitch threads and have a smaller 15/16" O.D. (see image).