You can just clean the EGR port ,but the port will clog again. If you install the pipe in the intake it will FIX the problem so that it doesnt clog again. So it just comes down to a money/time issue. Do you want to pay $350. to fix it or clean the port yourself every 50,000 miles or so?
Also , if you just clean the port you dont have to completely remove the intake or seperate the throttle body from the intake. Just remove the 8 nuts and bolts from the center of the plenum, the lift the plenum up and clean the port near the throttlebody. It only takes about 20 minuets after a little practice.