Updated List eff. 7/12
3@ Evil Shrine (pink area all 3)
1@ Metal Fortress (river of blood 2nd floor near Metal God location)
1@ Zarmazari Breach (in SE corner of last area with all those dark chasms before the Boss fight)
2@ (3?) NW Drone building (this is tricky, so save and read @Rabbit's/@Lady_JJ's comments below)
Basically, before entering The Pit; if you play Jukebox Song #2 then go find Kranko near Sandy, you can then possibly play Jukebox song #4 and find him again? It seems like you may be able to find Kranko a third time after returning from the Pit, too.
I do not have a save that can test this hypothesis, but that would mean it might be possible to find Kranko 8 times (I only found him 7 times).
Note: The last encounters in Drone were incredibly intense (he now has 25k-30k HP). Kranko had also increased skills that wiped out 2 party members regardless of resurrection and items. Kraken was the only 1 left alive and with only 125 HP. Expect to die. But there is some luck in what skills he uses.
Does that match what other people know?
One thought I also had regarding Kranko is that he drops lots of swords that I sold. But what if keeping those swords is the key to solving this puzzle?

Note: Keeping the swords doesn't seem to do a thing.