Exhausting the workbench just means collect all of the recipes (netting you the Prepared achievement) and then crafting every item. There are 64 recipes in the game.
Going through the game normally should get you most of the materials that you need but some of the harder materials to get such as Holy Energy and Dark Essence can be bought at various stores. The underground market that is accessed through the ATM in the dunj is the cheapest place to buy things, buying tons of steel and then buying the items that you need works fine.
I ended the game with an EXTRA $1000 after having everything crafted, so I wouldn't worry too much about running out of money. Holy Energy and Dark Essence can also be purchased at El Granero store in town and Glue and Fabric can be purchased at Championne Athleisure, also in town.
If you're going for the Polyamorous achievement, you should have tons of extra materials by the end except for maybe the very rare ones. Good luck!