With the help of my wife I was able to flush the clutch and there was some air but not a lot. The pedal doesn't feel solid and I can't engage the gears. There's quite a bit of pedal travel before I am able to start the car.

My comment might be completely irrelevant to your MINI problem...

The clutch pedal in my Jeep Cherokee would not return after downshifting...tow truck to Jeep Dealer where I told the shop manager, "I know nothing about the Jeep's pedal box, never had one apart, but I think it's a pedal box problem."  Patting my head the shop manager said, "We'll find out when we get in there."

Next day, the shop called to say the Jeep had new clutch installed but they were having trouble bleeding the clutch hydraulics.  Jeep would not be ready for pickup as planned.  Wait for it..."I told you when the Jeep was dropped off yesterday, I thought there was a problem with the pedal box."

Yup, broken weld.

What about the one under the driver's side dash?

Unfortunately, it is difficult to diagnose this remotely.  Could be an issue at several locations:

clutch slave cylinder
clutch master cylinder
clutch guide tube
clutch pressure plate
clutch release lever (inside the clutch housing)

The clutch hydraulics are fairly straight forward.

However, if the transmission needs to be dropped, that is a 12 hour job....

Ken

 

I could start the car when in first gear without the clutch working, but not in second gear.

I don't know much at all about new MINIs, but from what you describe, it sounds as if the pedal or linkage is binding. Generally, I think a failing master cylinder would prevent you from disengaging the clutch and stay that way. Check first for obstructions at or near the pedal, then at the other end at the clutch lever for something obstructing it. In any case, I imagine a master cylinder replacement would be much more complex than on a classic Mini. There's probably computer issues to deal with, I suspect.

On my 2004 Mini S, for a few weeks now, every now and then the clutch wouldn't return and because of that I couldn't shift into gear. This only happened at slow speeds. I figured out that I could pull the clutch pedal up with my foot and everything worked fine. So this was intermittent. When I was out yesterday the clutch went to the floor and pulling the pedal back up didn't help. I figured the piston seals went bad. It was a real hassle driving it home in 1st year, especially at stop signs (I avoid stop signals). I have not done this type of work, but I am asking what do I need to do to fix the issue and is it a difficult process? I am guessing I just need to replace a master brake cylinder, but I don't know, so I am asking for you guys to give me direction. I could take it (flat bed it) to a mechanic and he could do the work for about $300-400 or I could since the mechanic says he's busy for the next 3 weeks.