Same here- removed mine last Monday and noticed the same. If you wan to spend a little more than the 20 bucks to have it removed- throw on a new muffler for a nice sound. I haven't done that yet but I hear it fixes the rasp prob. Course if you really have some $$ fork it out for a new exhaust system. Check out perfomancefords.com- I am buying one of the mufflers there. Your choice- quiet system or loud. As far emissions- not sure- I don't have to go through that where I live- you might ask your local muffler shop- or I am sure someone on the forum knows. The shop can be fined if they do anything that doesn't meet the standards. They do have ways of getting around this though.
