STEP 1: Gather materials
This tutorial will start after the brake ducts have been installed on the car. The method is the same for any car and follows the same basic principles. Make sure you have aluminum flanges for your dust shield, high temp brake duct hose, and the necessary amount of hose clamps. Small bolts and screws will also be needed to attach the flanges to your dust shields.
Step 2: drill through fender liners
Using your hole saw, drill a hole in your fender liner to route the hose through. Do it as close to the inside of the car as possible (gives more wheel clearance) and in line vertically where you plan to mount the aluminum flanges on the dust shield.
If you have a cold air intake (not shown), route above it and through the headlight brace. If you still have the OEM air pump on the drivers side (00-05 S2000 only) then you will have to route below it. I highly recommend doing the air pump delete. It drops a good chunk of weight and deletes unnecessary clutter in the engine bay. I don't think there is a cheaper way to drop weight on the market.
step 3: route to the back of the dust shields
Route the hose as shown below to the back of your dust shields. Try to hug the inside wall as close as possible to allow maximum wheel clearance and alongside the upper control arm.
Step 4: install aluminum flanges
For this step the calipers and rotors will have to be removed to access the dust shields. Using your hole saw drill a hole as close as possible to the center of the rotor. I made sure I can fit the aluminum flange in that position first by holding it to the back of the dust shield. Be very careful with the ABS sensors when working in this area. I took a clock towel and covered it so any debris would not hit it just to be safe.
After the large hole is drilled, mock up the flange and drilled some mounting holes for your M6 or similar screws. Once holes are drilled into your dust shield transfer them to your aluminum flange. At this point you can attach the flange onto the dust shield and put your brakes back on the car.
The final step is to use your hose clamps to mount your hose to your aluminum flange. Make sure to go lock to lock with your wheels on to check for rubbing. Reroute hose if possible, but if you cannot avoid it then cover those portions of the ducting hose with duct tape.
Detail 6: finished!
Make sure everything is tight and torqued and put the car back together.
Refer to the pictures if you need help routing the hose or where to secure it. In the picture below, I am running 17x9+45 wheels with 255/40/17 tires and I do not rub at all with 2.5" hose.