My $0.02
Don't use a Dremel on it - very flawed idea, from both a vibration standpoint, the fact you STILL won't know it is making connection below,limited room and attachment material inside, and unavailability of those crystals(I and others have them, we harvest them off modules that keep good time but have display/logic issues).
The little contact in the negative down battery well. Pull off the plastic battery retainer ring and file the plastic where it comes up to the little bent "ear" of that battery clip - just a few mm. then put the plastic ring back on and bend that ear up a just a little more(the plastic ring will support it against breaking off the board). If a battery pushed in doesn't fall out when turned over, you have it just right.
The quartz crystal will come off the board easily .
With the plastic ring off(of course).
Hold your non-dominant hand palm up, hold module around edges firmly(no pressure on front plastic, there ARE wire-bonds below it), place your thumb between the two battery contacts to further spread the force out,
push the top of the crystal toward edge of board(like you are tipping over a tombstone or a drunk...sorry, only visual that came to mind, teenage hi-jinks

). Stuffing a little silver epoxy in the holes is fairly easy, you just pull the epoxy to a nice fine tip by dipping a thin needle in it, cram into the holes in the board.
Don't blob any at all outside the hole. If it gets messy, stop and clean the entire area very well with a little isopropyl alcohol on a cotton swab. A few errant grains of the silver could drive you crazy with the symptoms. When you have them crammed fairly full, stick the quartz crystal in and let sit for a few hours. If successfyul, place a
small dot of regular epoxy at the base to secure the crystal to the board better. It's not rocket science, just takes a little technique.
Last thoughts: Take a little Lime-Away(or similar product for removing lime and rust stains from toilets and sinks and using a cotton swab, clean the entire boards surface and that plstic ring of any stains from batteries leaked in the past....those disolved metals can cause weirdness. The aluminum battery contacts can be saved from oxidizing by using a little electrical contact cleaner/protector on a cotton swab.