The only holes I left were originally for the A/C (where I plan to run my engine harness, which ends up unseen behind the intake), the steering column and the brake booster. I filled everything else that I didn't plan to use. I'm going to run all of the wires for the front (lights, fans, etc.) inside the driver's side fender and come in through the kick panel area so you won't see any wires.
Should be pretty clean when I'm done.