Pro tip: go for as many blues as you can, as they're worth 10 greens. It's totally fine to leave plenty of greens lying around, but get as many blues as possible. And whites too, when it won't kill you to do so, since they're worth 100 greens.
Okay, after trying for about 6 hours to kill Phantogod with full upgrades and max runes, I "won" when he glitched out with most of his health remaining. I highly recommend toning down the minions near the end of the battle.