pberboy,
I don't think you want to start drilling your case until you get the board fully assembled. For one thing, the pot hole has to be PERFECT since you have no wiggle room once you select a slot.
The Millet was my first real case job (other than mint tins) where I had a board mounted panel part and I was very nervous about mis-placing the pot hole. I laid out the panel in Front Panel Express, printed it out, carefully cut out the panel outline and the holes and taped it on the case with the board in place. Then I could place the Neutrik jack in it's hole and see exactly how it fit relative to the board parts. That jack can be very tricky to place because it is a huge 15/16" cylinder sitting inside the case on top of the board. It may not be obvious from my picture but the solder tabs on the jack can encroach on the cap immediately behind it, especially if you use a Cerafine or other large cap that fully fills the board outline. The neutrik is a nice jack (I like the locking feature myself) but it is tough to place on a panel. I am about to case up an M3 and I am going thorugh the same exercise because I can't put it exactly where I want it and I will have to work through a paper panel exercise to get it right.
Another thing you cannot see on my images is that the Neutrik jack sits within 1/8" or so of the board if it is vertically aligned with the pot. If you are off even a little bit, you will have a problem. If you line them up exactly on a horizontal axis, it should fit.
If you want the pot knob centered vertically on the panel, as I did and most people do, you have to use the 2nd slot. The pot is soldered to the board so it's elevation is a fixed distance above the board.
You probably want your tubes to stick out further than mine, for example. You cannot do that without either placing the pot and HP jack well above center OR you need to somehow raise the tube sockets. I thought about that myself, because I think it would be neat to have most of the tubes exposed, especially since the internal tube parts block most of the light from the LEDs that we put under the sockets. I gave up because I wanted the get the thing built, and built right without some weird hack to raise the tubes.
If I were going to raise the tubes, I think I would get some very stiff insulated solid core wire- the thickest wire that will fit in the tube sockets, which have very large pad holes. I would make 1 - 1.5" lengths (however it measures out) and solder one end to the tube socket and one end to the corresponding board pad. I don't know if there are any adverse consequences to doing this, but I think I would try it if I ever make another one (and I have a couple spare boards). I don't recall anyone else doing that with a Hammond case.
Even on the back panel, where the panel parts are floating, you have to work around the caps and other parts on the board. I had to do a lot of planning (after the board was stuffed) to be sure nothing interfered. I had a particularly difficult time placing the three probe sockets (which is at least somewhat unique to my own build) because the layout dictated the placement, which was not where I really wanted them.
One other suggestion.... I sucked it in and bought a 15/16" Greenlee socket punch. It cost me about $40 from Mouser, I think. That punch fits the standard Neutrik "fat jack" holes and if you ever decide to use their RCA jacks or Powercons, you have the punch. I also used the Greenlee to punch the tube holes in the top panel. I think it was recommended in the build instructions to make a 1" hole and if I had a 1" punch I would have done that. I measured very carefully, setting up a template in Front Panel Express software (which I use for every case panel I have drilled) and I was right on the money. It is a very tight fit. I could have tried to enlarge the holes a bit but that would have hacked the perfectly smooth holes that the Greenlee made. It is expensive but it is a very nice tool. If you mount the Neutrik like I did, with the plate inside the panel, you will want a very smooth 15/16" hole. That is tough to do with a hand drill.
I also used the Greenlee punch to cut a vent hole over the regulator heat sink on my Steps case. I punched two holes, such that the edges of the holes just touched. I then ground down the "points" where the circles met. By doing that, I only had to make flat edges and I was able to leave the rounded edges of the oval as punched. It is much easier to file down a flat edge than to try to make a nice smooth oval. It would have worked great if I had not slipped and marred the surface with the spindle of my Dremel, which I used to flatten the edges. I did get a decent oval and I think the concept is sound. Eventually I hope to source some acrylic and replace the top, and include holes over top of the bias pots. It is a PITA to have to remove the cover every time I roll tubes and rebias. If you want to expend gray matter doing something fancy with the case, spend your time thinking about how to best roll the tubes and rebias.
I kept my FPE diagrams for the top, back and rear panels. I would be happy to email them to you if you think it might help. As far as I can tell, I drilled my case exactly per those diagrams and I was happy with the results and everything fits.
Regards,
Neil