1991 Power Ram V6 4x4

Hearing a little knock that repeats at the same pattern when in neutral. When clutch is engaged, no sound but I do hear some whining. Also, clutch is having trouble engaging in first gear, seems like it chatters a bit before it catches. Also, clutch pedal went to the floor and I had to lift it up manually. Notice clutch fluid was empty, filled it up, problem no longer there.

Here's what I think:
Clutch pedal to floor
Conclusion: Leak is happening at the master cylinder or slave cylinder. Going to replace both.
Chatter before fully engaged in 1st gear, clutch not fully engaging, replace clutch.
Whining noise when clutch is engaged, throw out bearing.
Chatter when in neutral, I don't know. I really hope it's not a chipped gear.