On a '99 Subaru I had, the cast alum. snout on the transmission was badly worn at 60K and it had a stainless steel 'repair sleeve' installed on it. I doubt the slave cylinder (very easy to access) would cause your noise issues, but it might cause engagement issues. You could also have a combination of a bad slave cyl. and iffy throwout bearing. I suspect pulling the trans will be the only way to really see what's going on.
You might take it to a Subaru shop for a parking lot drive-and-listen session and get their guess as to what is wrong.
Steve H. - KE0KNH
Colo Springs, CO
'78 FJ40, '89 FJ62, '98 4Runner