I'm cutting the step on the lid here that will mate-up with the bottom. Here I'm using a 1/2" diameter cutter to rough the step in with.
 

Another Problem

On a side note, here is another area that needs to be addressed from my sanding episode. See that miss-match, that just won't do. So...because of my bad sanding, I'll need re-cut this area again later.
 

Machining Again

What I'm doing here is finding the exact length from one side to the other (of the steps) on the bottom piece. Once I have this dimension I can cut the top to match. Now my 12" calipers are too small to measure across the steps by them selves so I'm using some 1" X 2" X 3" blocks to help me. BTW, I'm using my granite surface plate to make sure things sit flat.

The two outside blocks are against the step (that I want to measure), and the the two inside blocks are against the other blocks. This gave me just enough distance between the two inner blocks to use my calibers and get a measurement.
 

I'm using a 1/8" diameter end mill to finish the corners with, so it matches the radius I filed earlier. Once I unclamped the lid I checked the fit and it was exactly what I wanted. I went with .010 clearance, which should be more than enough once the clear finish has been applied.
 

A couple of days later I was messing with something and placed the lid on the box and for some reason the lid warped. But I don't know why this happened and now it doesn't fit correctly. See the 12" scale sitting on the top? See the 18" scale under it? And see the 12" scale is touching the outer edges of the lid? Well...that scale is .030" thick, which means the lid is bowed by that amount.

At first you might think, 'no big deal, nobody will ever see that'. However, what you my not have noticed is gap at each end where the lid touches the box. That gap allows the lid to rock from side-to-side, which isn't good. It's not good in my book anyways, not good at all. One step forward and two steps back...
 

Re-Work

I put the lid back on my milling machine to re-cut the areas that were a problem, which is between the two spots marked 'Low'. I needed to cut the top and bottom of the step so the lid would fit correctly again. However, only the two ends needed to be reworked (not the long sides) so it could have been worse.
 

More rework: As you can see there is a large step at the top that needs to be fixed. This is the result of me sanding too much earlier. To fix this I'll be cutting the sides with a long end mill. That's the good news, but after the bad areas has been machined away, I'll end up with the lid not fitting because now it will be to large.
 

This is the opposite end of the same side from above. I stayed away from the end by an inch or two and then stopped, turned the box upside-down and then re-cut this area so it blended.