Instead of counting holes on the PCB, I used a piece of paper as a jig.
All the top LEDs are rested in the holes of the wooden jig. It was standing like this while I solder all the cross wires.
Foam core board is my friend. A very simple jig made of foam core with slits cut using a razor blade. Holds the wires at perfect 4cm spacing.
This small screwdriver was just the right weight to lightly hold down on the wire that I'm soldering.
I like how the cube looks when you're looking down the "aisles" rather than straight on the walls. So I decided to make this the front of the cube.