Haven't built any DEFX, yet, but regardless here's 2¢...
Sometimes I don't like the layout intended by a PCB's creator, so I get the enclosure and just shove the unpopulated PCB in it, turn it around; I consider offboard wiring some pots or switches while still having others remain board-mounted to secure the PCB.
I'll even flip the PCB and if built that way the components are hidden (or I'll populate on the "wrong" side except for ICs). Sometimes that gets the pots in the position I want, ie extending away from the board and not hovering over the board, by repositioning the pots on the flipped PCB the correct legs of the pot still line up with their intended spots on the PCB and thus preventing a control that works in reverse. Why bother? For top-jacks, or to accommodate a graphic, arrange controls in a more logical-to-me way...
I hope all that makes sense.
I use a set of digital calipers, and I just measure things and map it out on the enclosure itself; every build I've ever completed has deviated in some way so I've never used a drill template as anything but a guide (Low Tide might be the first circuit I build stock).
So, lots of planning, measuring, more planning, mocking up pots and jacks in situ, then more measuring and planning.
Take you time.
Use a drill press if possible with bits only used in the press, never used in a hand-drill.
My hand-drilled enclosures didn't turn out as well as those done with a drill-press, AND hand-drilling tends to bend/warp the bits (for me at least) — hard to get any accuracy when the bit is wobbling around. Now I need new bits for the drill-press — after hand-drilling you can plainly see the bits wobbly-wandering even if in the chuck of the press.
The DEFX builds are often larger than need be, IMO, so while I love the DEFX PLL and plan to get it, for something like the Engineer's Thumb I'd opt for a tighter layout such as offered by PPCB. No room in many of the DEFX layouts for mods, extra switches or stompers.
I know there's a few people here who've built DEFX, hopefully they weigh in.
