* I got a gem from Kazuro (final boss) fight, and I think Lady Shiori's (pre final boss) also dropped another. Haven't tested if they drop on subsequent defeats.
* Quality upgrades: upgrading to "transcendent" quality isn't as worth as earlier levels. The more stats on the item the more profit from quality upgr.
Each gem raise by two "levels", gold by one "level".
* Unlike normal gear perks - gem upgrades do stuck. There is an UI limit of 8 perks displayed - don't worry all perks still work and provide You with their blessings ;)
* The obvious point: I think it's best to save them for items later on. Just note their locations - don't grab them and clutter inventory ;)