new member - 2001 VW new beetle, manual transmission

We are getting ready to do some clutch work on our 2001 new beetle. Our car has been sitting for nearly 3 mos now. My 17 year old daughter was driving it one day, when she said the clutch pedal went all the way to the floor and there was some smoke and a burning smell. Once we got the car back home, we discovered all the brake fluid had leaked out and determined it was the slave cylinder. We replaced the slave cylinder and hydraulic clutch line. Now the clutch is making a chattering noise and appears to still be spinning even though its not in gear. When attempting to change gears with the stick shift, there are grinding noises. Any advice or tips would be greatly appreciated..