manual transmission noise
 

Bought my wifes car about 2 years ago and she loves it. Having a few problems with the tranny. Wife does not know much about cars or dealers so I said "take it to the dealer watch what happens" They charged her around 3 hundred to look at it and change the oil. Quoted her about 5k for stupid crap like seat sensor, radiator fan, engine mount, spark plugs, wishbone bushings etc etc and couldn't really advise her on what was up with the tranny. They said they need to pull it off to investigate. Well anyway I said hell to the no for anything except change the oil because I don't fancy trying to find somewhere to dump that crap. I'm kinda enviromently friendly in that respect. Although looking at BP's disaster 4/5 quarts is nothing. Anyway I repaired my wifes car for about 1200 dollars from various parts off the web and all is good except she still has a transmission issue. There appears to be a rattle noise coming from it which might just be the thrust bearing or pressure plate and it's difficult to get into gear at junctions. But I've been looking through fourms and seeing people change out quaifes and bearing seals behind the flywheel transmission seals, gaskets , but looks to be the older ones. My question is would there be a problem in the actual transmission or can do you think I can get away with just changing out the pressure plate/thrust bearing? It's a 2006 cooper with 80k miles on it.