First, drop that sucka!
You are lucky enough to have the power of the entire Subaru aftermarket at your disposal. You can choose from a variety of springs, struts, or even coilovers.
Second, there should be aluminum skidplates available for your car. Most Subaru skidplates extend to the front jacking plate (under your steering rack). The engine cradle/subframe and exhaust manifold hang down in the breeze a bit. A skidplate will clean this up and insulate your oil pan a bit. Your car isn't going to overheat, but should run nice and warm just the way you want it for mileage.
Third, look on the Legacy forums to see if there are any factory parts to plug the holes when you remove your roof rack.
Next, look at your options for another bumper cover. There were several legacy models. IIRC, some Legacy models cam without fog lights. Some had a much lower front lip (built-in airdam). You're grille insert can also be snapped out and replaced with other models.
You can easily and cheaply space your hood if you don't mind the way it looks.
Other than that, you might want to check out the black plastic around the wheel wells. Both sides of the engine are blocked from wheel wells by plastic panels.