Currently, I have a CAI that goes into front of the wheel well. The purpose of this set up is to get cold air... but do the losses from having the air bend at 90 degrees into this area negate the benefits? If I just put the filter on the straight pipe connected to the maf and built some sort of shielding around it to prevent underhood air in, wouldnt that be a better setup?

 

Pressure is lost due to a number of design factors:
-length of tubing
-diameter of tubing
-roughness coefficient of tubing material
-bends, including how sharp they are
-sudden enlargements
-sudden contractions

It would take a fairly detailed fluid flow analysis to apportion the losses to particular features of the intake design. A more practical approach is to do a scan of the PCM, recording the barometric pressure, MAP and RPM. This will allow you to calculate the actual pressure loss between the outer surface of the air filter and the intake manifold plenum. If this number is unusually large, you need to start looking for the causes.

Obviously you can reduce pressure loss by straightening out the bends, making the diameter of the tubing larger, using a smooth interior surface material, minimizing changes in cross-section, etc. But based simply on a guess, I wouldn't assign a disproportionate amount of the systems air pressure loss. How sever this loss will be depends to a large extent on how much air your engine is capable of using.