Chris, you can remount it in the fender after your get your pipes done, if your inspection place checks it all it has to do it work, it doesn't have to be easy ti fill...lol I actually mount the radiator overflow in the trunk area all the time, this will prevent any fluid hitting the rear tires if it ever spits up, this is a must for a race car.
If you ditched that you can make the bends nice and smooth up to the intake, if you wanted you could actually bring it out through the panel that would be behind the stock battery location.
Look at the pic I posted of the ATI on the SN series car, the pipe leaving the blower swoops down, goes near the frame rail and then goes into the intercooler via a 90 degree rubber elbow. that same design will work for you but instead of curving to the blower you'll attach it to the intake.