Make sure the peddle to clutch system is working properly. Maybe the skid plate was gradually coming off which tweaked the clutch system adjustment. How does a skid plate just fall off?. $2,000 for a manual transmission rebuild sounds a bit strong (well, I haven't had one built in a while I must admit) and there is no better time than the present to learn how to drop the transmission yourself and only have to pay the labor for a shop to rebuild the tranny. Just my .02 cents.