Starting with your battery cover, looking at the outside, the button sets are going to sit horizontally in two of the recessed ridges of the cover. The L1&R1 button set will be in the second recess from the top and the L2&R2 button set will be in the very last recess.
Looking at the inside of your battery cover, you will see two horizontal supports. You will need to remove the top support (the one with the screwdriver aimed at it).
My method was to grind down the support until it was close to being gone and then going over it with an 1/2" (13mm) wood chisel to make it look as if it was never there. It's a good idea to scuff the surface when done because you will be adding small amounts of epoxy adhesive which does not hold as well on glossy surfaces.
When pressing your PCB inside the cover you want the bottom edge of the PCB to be resting on the bottom support of the battery cover (this is very important for the button alignment). DO NOT GLUE ANYTHING YET!
You may notice that the PCB fits a little tight within the cover. [This was done intentionally with a dual purpose. 1) not all battery covers are identical and as i said before, we can always take some material away much easier than we can add more. 2) a tighter tolerance will aid in securing the PCB and hopefully add durability during gameplay.] If your PCB fits too tight you will notice a slight concave in your battery cover...like this.
Do not worry. With a few strokes of a file or light scrapes of a razor blade, you can shave the side edges of your PCB to fit tightly inside the cover without a concave effect.
The amount shaved off the PCB will be few thousandths of an inch (or hundredths of a mm). You will not damage your PCB by doing so and, as always, BE PATIENT. You can always remove more material, if it fits too loose the epoxy will hopefully compensate.
After you have your PCB and cover situated, you're ready to drill. The holes on the PCB are pilot holes for the buttons. The holes are at the absolute maximum width of the buttons. Make sure the bottom edge of the PCB is butted up to the bottom support of the battery cover and drill your holes.
Remove the PCB from the cover and inspect the outside of your cover. It should look like this.
Very carefully with your dremel or drill, connect the holes horizontally within the recessed part of the battery cover outside. (I used the dremel to roughly connect the holes and my file to fine tune the slot.)
Be careful not to wander outside the recessed channel we are utilizing. The measurements allow for very little deviation. The button will fit perfectly if you stay in the lines!
Once your slots are cut, do another test fit with the PCB and verify the switches and pilot holes line up.
Remove the PCB again and insert your buttons. Be sure they move freely within the cut slots. If necessary, use your file to carefully shape the opening so the buttons move freely in and out.
When installing the buttons, you'll notice the pieces on each side are offset from the centerline of each button. These pieces are there to keep the button from falling out. DO NOT CUT OR TRIM THEM! When setting the buttons in the holes, make sure these side pieces are closer to the top of the battery cover. (I have designed this to give the buttons a slight upturn when fully assembled. This makes a big difference in the ergonomic feel when pushing the buttons during gameplay.)
Now that the buttons are set in the slots and moving freely, press your PCB back into the battery cover and give everything a test before gluing. The PCB should be sitting flush in the battery cover with everything fully assembled. All PCBs have been tested for continuity after soldering and before shipping. If there is an issue with a button not working, it is an alignment error.
Once everything is tested and you are confident in your install, you are ready for adhesive. I used a clear 5 minute epoxy. I know it holds better than hot glue and although it says "5 minute", i would let it sit overnight just to be safe.
When applying the epoxy or glue, focus on applying some on:
-the sides between the PCB and cover
-the bottom corners and overlap on to the PCB
(I'm limited on post attachments so I'm recycling images)
use caution around the bottom edge of the PCB. You don't want to glue the button into the slot!
note: no adhesive is necessary at the top of the battery cover, the DMG case will hold it in up there.