First thing is to upgrade favorites only, then non-cageable, then cageable. That way you can use other peep's stones for upgrades.
I did bag dailies every day from soon after MoP release until a few weeks before 5.3.
I did world fights in areas with the pet type I needed stones for, mostly focused on flying, critter and beast. Pick a spot near a stablemaster.
For flying/critter I farmed in Mount Hyjal, easy access to 22-24 critters and stable master.
For critter, I farmed in the Valley of the Four Winds, kind of in the farm area west of Halfhill.
For Beast, Krasarang Wilds is good. Allies have a nice spot at the Incursion, I forget what the name is for horde.
I also traded stones with peeps, offering 2 for 1 when I got down to my last few. I also offered in trade on my server to buy general stones for a more reasonable than the AH price, and paid for the use of stones. I probably paid too high, but it got me what I needed (and I used to have a decent amount of gold