I have a very early build date 04 and yes I have a little 2-3 grind first thing in the morning. It goes away as soon as there's a little heat in it. I don't view it as a big problem but I had my Ford dealer take it for a ride. They said it was normal, but I made them state my problem on an RO so I have a history on it. When I get closer to 36k miles I will persue the matter further and make them fix it. It's really not too bad but hey if I can get a new trans out of them, so be it. The OASIS report on my car says "Some 2004 Mustangs equipped with a TR3650 manual transmission may exhibit a hard to shift condition. Engineering is aware of this concern and is investigating. TSB 04-15-06 does NOT apply to 2004 model year Mustangs." The report also states "Until a new repair procedure and/or parts are available, proceed with normal diagnostic and repair procedures. Monitor OASIS for updates"
So to answer your original question, Yes, you may get an 04 trans that has the same problems the earlier models have. Hope this helps you out and clarifies Fords position on the 04 trans.