I had this same problem. The clutch was squeaking like crazy. It was coming from the transmission/slave cylinder area. Is that what yours was doing? I took the slave out and greased the little tip of it hoping to quiet it down. Didn't work. It still squeaks and my clutch feels a little stiffer than others I've felt. You say the master cylinder? Did that affect your brakes as well? My '00S only has around 40k on it but the squeaking (more like a creaking) drives me nuts.
sean
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