So I've done a total overhaul of my Agile AG-3000's wiring, and have all of the signal-related hookups done, leaving just the grounding joints. Grounding is something I'm not so sure about, as the Duncan diagram just said what needs to be grounded, not where.

All grounds have to lead to the jack's ground lug, right? Would this scheme here work?

And also, when soldering two leads to one lug, it's acceptable for the two leads to touch, right?

A thousand thank you's to anyone who gives a damn.
Doesn't matter where you ground it, it matters that you ground it, i.e. connect all the grounded wires are connected. The wires going to the back of the vol. pot are connected together, and then all sent to the jack's ground through the back of the pots which are also wired together.

And regarding your last question: Yes, because if the leads don't touch, the signal flows from one wire through the metal lug, into the other wire. Same thing.
Schecter Hellraiser Deluxe
Boss DS-1
Crate GTD65

GAS List:
Mesa Boogie Dual Rectifier Roadster