I explain all metalwork in the "Enclosure preparation" step. There are drilling templates that aid in marking the holes location. These are A4 drawings outlining the exact location of 4 modules placeholders inside the case. Print out these PDFs (make sure you have NO scaling in your print dialog). Make sure that mouting holes on the paper align with the mounting holes on the module motherboard. If not - there're some issues with the printer scaling that you need to fix.
On the templates there's an outline of the enclosure lid. Cut out the template using these lines as a guide. What you'll end up is a piece of paper that represents the enclosure lid with modules mounting holes marked. Now you need to fix this template to the enclosure lid. I use a paper masking tape for that. Make sure to align the edges of the template and the actual lid. Also, there's a screw hole on the template near the edge - make sure it's aligned with the actual screw hole in the lid.
After fixing the template to the lid use a center punch to mark the holes. Now you can remove the template and drill the holes with 3mm drillbit. If you plan to install all modules I suggest that you drill all holes - this will make your life easier and you won't have to drill an enclosure with electronics in it or unmount everything to drill some new holes.
You can also check out the metalwork page in the RN73 guide. It uses different templates, but the procedure is the same:
https://www.rackneve.com/1073Guide_METNow, regarding modules placement. I place all signal processing modules to the left, and the PSU board goes to the right (this is if you look at the enclosure from the front).
I'm using threaded rivets instead of stand-offs, but they require a special tool to install. If you have that tool you'll need to enlarge the holes to 5mm so the rivets will fit. If you're going to use stand-offs, no more drilling is required. Just screw four 5mm stand-offs to the mounting holes and you're done. Since the stand-offs are so short, you'll need to use very short screws so there's some thread left for board mounting. Another option is to use a long screw so that it goes all the way through the stand-off. This way you can secure the board to this same screw with a nut. Yet another option is to use male/female stand-offs.
As for module stacking, this is explained in the "Assembling the module" step, the very first photo. Take the motherboard, screw it to the stand-offs. You'll need 2 screws and 2 15mm male/female stand-offs. The stand-offs go under the marked screws on the photo - you fix the motherboard with the male part of the stand-off, on top of it you have a hole for fixing a meter board.
Let me know if anything is not clear. I'll see if I can make some photos of the module.