You aren’t doing this before you gain the ability to duplicate.
Before the very final moments in the game, your options are not fantastic. An easy one to set up is Zettel -> Super Steel Gear, for Synth Quantity +1.
A better one is Poison Cube, but I need to explain this a bit. You need to start from Flour, recipe morph into Poison Cube, then get both Add (Fuel) and Synth Quantity +2. Doing it like this lowers the level of the Poison Cube from its native 20 to Flour’s 4, thus reducing the gems necessary to duplicate.
I’m sure you know where this is going now; you simply duplicate your Synth Quantity item, then throw it into Super Steel Gear as much as possible. You’ll have a reasonable amount of gems to work with after a few repetitions.
For endgame, you’ll have access to the Philosopher’s Stone, and there’s an extremely abusable loop involving it. You make a Red Stone with Synth Quantity +2, duplicate the hell out of it, then you just cram as many of them as possible into a Philosopher’s Stone. You’ll have a ton and you can max out your gems stupid quick this way.
With 9, you make 19 Philosopher’s Stones. With the traits it turns to rank S. You'll be running over 100,000 Gems per run with this.
Thanks for the Poison Cube strat. I was looking for good gem farming guide because I still want to face the last boss with full items but farming is difficult.