Sean,

Run the seafoam through it, using 2 bottles (1 bottle exclusively for your intake cause the manifold seems to collect a lot of sludge) and let us know how its working after a complete tank of gas. Basicly your gonna do the seafoam in the intake 4 times over the course of the tank of gas, do it like every morning and then drive to work and back till the tank is gone.

You could just have a lot of crap bult up from the years of use. If that doesn't help then start looking deeper. Don't install a cheep restrictive CAT just take it back to the store and get a high flow one. Don't try to reuse the old one either cause you'll never get it back, you have to understand the extreme temps that build up in there when they clog, if you look at one it will be glowing red hot. While your at it get a cat-back system put on if you like with a 2.25" - 2.5" progressive set-up.