It could be the ring gear. I had a grinding/clacking noise, which sounded like the starter didn't stop spinning for a second or two after the car started. It turns out the ring gear was bent. I think it can get bent when you remove the transmission. Some techs try to pull the ring gear off with the transmission, but it is supposed to stay connected to the engine. Anyway, to get that replaced, you have to remove the transmission. I also had my starter replaced at the same time. I think it cost me $1000 or so total, parts and labor.
You can search ring gear, and there should be some other info...but just make sure that it's definately the problem before you replace it, as it's expensive and surely a headache.