The way to check if the filter is clogged is to do a fuel pressure test. It's rare that they clog up unless you got a really bad tank of gas or someone dumped something in your tank. FYI, these engines normally idle a little rough by nature. The idle can be bumped up a little, which helps, but you need either a capable scan tool or a tuner (i.e. Bully Dog GT) to do so. Also, to make a note on the above post, you can rule out EGR valve as these engines don't have one.