yes, if the reservoir went dry - it definitely may have introduced air into the lines...

Is it possible that there is air in my clutch master cylinder? By the time I started repairs the brake fluid recovery tank was empty and I have reason to believe that the brake master cylinder was also low or empty. Could that have lead to air getting into my master cylinder?

If the gears will not dis-engage with the clutch depressed, and you can see the slave extending with the pedal, then it sounds like maybe the shift lever inside the housing is broken / bent, or the throwout bearing is gone.... 

In either case, you may need to drop the transmission to take a look inside...

All three times I bled the cylinder it was fully compressed using a jig. Should I now try installing the cylinder uncompressed?

When I press the clutch pedal it is spongy but the clutch isn't engaging or disengaging. If I put the car into first gear and push the clutch pedal down and start, the car starts in gear, jerks forwards then stalls.

The clutch should only have about 10k miles on it give or take 3-5k.

We recommend you bleed the clutch system once with the slave fully compressed, and then again with it installed in normal state.

When you say the clutch 'isn't working at all' - is the slave operating correctly when the clutch pedal is pressed?

How many miles on the current clutch?

A while back I dropped my 2006 mini cooper s off a curb and I broke my slave clutch cylinder. I replaced my brake master cylinder and the brake fluid recovery tank. I've bled my clutch slave cylinder 3 times now taking it off and putting it on again, each time the clutch is still spongy. I don't know if I broke anything else but I can't seem to figure it out. Also not only is the clutch pedal spongy the clutch just isn't working at all. Any help at all would be nice.