I was thinking last night about this and the only sensible conclusion I have come up with is that the 2 birds refers to defeating Judy and saving Laura.
The clues could also be directions on how to find Laura, in which case the final direction is arriving at Carrie, and realising Laura is buried inside her: "2 birds (Laura/Carrie), 1 stone (one body)". If Luara/Carrie is some kind if weapon then "stone" is appropriate.
Or it could be 2 waitresses, 1 address... thinking about this clue is maybe what motivated Dale to ask if there is a second waitress.
Maybe the message to Cole is a red herring, meaning each of the 3 clues has 1 matching red herring in the main narrative.
Who knows!
I kinda think Laura is the stone and maybe BOB and Judy are the birds. The Fireman is not just concerned with our dimension, but multiple ones. Metaphorically, he cast a stone into those worlds (the Laura orb) but needed someone (Coop) to help lure the birds (BOB and Judy) into its path.
The other thought I had is just that there are two problems that the Fireman is trying to fix and Cooper plays a role in both. We mostly know only about the first problem centered around Twin Peaks until the end of Season 3 when we get a glimpse of another alternate reality. The Fireman wants to solve both problems and devises an economical way to do so via Cooper.
Fire walk with