Make sure you put a cotter pin in that pin NOT a spring clip.......................................

I had a 1/32" crack develop between the ball and shaft that rendered my otherwise working clutch useless. I couldn't believe that such small gap would have such big consequences. I'd post a pic but haven't been able to post pics for the past couple of weeks. But yeah, it sounds like your troubles are hydraulic. After you sort it out, consider a new arm and ball. MED Engineering and MiniSpares offer an aftermarket billet version that's considerably more robust than stock. Good luck.

Yeah i think (hope) your right that the problem isn't internal. The only clunk can think of would be the throw out stop/locknut slammed into the flywheel cover. I've got the cover of and it makes a pretty loud bang which could sound like a clunk when attached to the engine. I just took apart the linkage and the shafts & pins all give groves worn into them, but nothing's broken.

Externally, the slave shows the same amount of wear as the rest of the linkage but nothing appears broken. The master hasn't lost any fluid. 

I may as well replace it all while I'm working on this. 

Of course while i was writing this response, I decided to check the pedal as per your suggestion. It appears to have lost the connecting pin. The pedal now has about 50% travel before making contact. I guess that's what the loud bang was. 

Oh well. Still going to replace these worn out parts.

The 'pressure point' felt at the pedal (where all the slack is eliminated and you are actually applying force to the clutch) should be somewhere around 1/3 to 1/4 from the top of the pedal travel. A worn clutch would make that point higher, eventually to slippage without pedal action. So, I doubt the problem is internal to the clutch. Loose or broken engine mounts should not affect clutch action since the slave cylinder is mounted on the flywheel housing. That pretty much leaves the problem of low pedal somewhere in the actuating mechanism - pedal, master cylinder, slave cylinder (and bracket), push rod, lever, plunger and release bearing.

A single, non-repeating "clunk" suggests something broke or slipped. (A repeating clunk every time you press the pedal would suggest something binding.) So, go through everything listed above, checking for wear or damage. Start with the visible - pedal actuation, slave cylinder and bracket secure, push rod not bent, etc. Check the lever pivot hole and pin for wear - a little wear is magnified by the arm length to where the slave pushes on it. If the ball is worn, it would leave a lot of slack by the time you get to the pedal. The pocket the ball sits in on the plunger could also be worn. The plunger might be binding. Release bearings generally get noisy as they wear out - they should make no apparent sound with the engine running. If your release bearing did fail it might be noisy and/or it might have gone beyond that to the pint of being worn down.

Did you look for a leak under the dust cover on the slave cylinder? Did you feel the bottom of the clutch pedal for a leak?

Bleed the system and if the clutch improves you have air in the system and a leak somewhere. 

If there is no improvement you probably have wear on either the pivots or the main linkages.

The ball at the end of the shaft the slave cylinder pushes on looks a little worried but not broken. I don't know that it would cause those issues immediately rather than slowly over time?

Before ripping into the clutch, remove and inspect the lever the slave cylinder pushes on. Its pivot pin may be worn or the ball on the end may be worn or broken. shifting into 3rd and 4th may be easier because they are spinning faster and the synchronizers have an easier time.

Hi y'all, Im having a ( verto )clutch issue. When I pushed in the clutch pedal to 3->2 downshift, I heard a thud and it became difficult to get the car into gear.  Shifting into 1st and 2nd is VERY difficult now. The pedal is also soft. I also found it isnt disengaging completely. When I was sitting at an intersection, the car slowly moved under power in 1st with the clutch pedal pushed to the floor. 
Shifting into 3rd and 4th is easy. There was no need to force it into either gear. Though the pedal still needs to be pushed to the floor.

There is also no leaks between the resivoir and the slave cylinder. I saw the slave is still pushing the plunger with help of someone else pushing the clutch. Is this a simple adjustment issue or do I need to rip apart the clutch? Thanks for any help.