I also have 2 conquests - the 2003's transmission is much less noisy than the 2000's. I bought the 2000 after the 2003 and soon after I got it I took the tranny apart to inspect it. I expected to see some damage and found absolutly nothing. I've got another 100 hrs on it and its just as loud and works just a well.
Typical signs of a bad tranny's I've been around (only two) are they jump out of gear or have a lot of "back lash" sound when you go on and off the throttle (much like a bad rear end in a car).
Sounds like you are just fine.