Utah YJ, Your jeep looks sharp in the avatar above, what kind of lift do you have?
Hey thanks for replying to this post. I should have replied, I ended up answering my own questions re: the jeep's clutch. Fortunately for me, my issue was the clutch master cylinder. Before taking it in for a full clutch repair, I decided to replace the clutch master cylinder first. I bought a replacement clutch master cylinder from O'reily for about $40. It took about an hour (well an hour and a half, see below) to replace the stock unit. The new master cylinder is metal body, whereas my factory one was plastic. The master cylinder gravity bled for the most part, and after purging the line of air I have not had any additional problems with fluid level or clutch pedal pressure.
Tip: purchase an inexpensive metal punch in the same diameter as the roll pin hole while you are at the auto parts store. The hydraulic line has a pressure fit bung with a rubber o-ring; the roll pin is driven in over the lip of the bung to seat the o-ring into the master cylinder. The roll pin is about the same diameter as a finishing nail, which might also be used to drive out the pin from the old master cylinder. BE CAREFUL not to drop the roll pin; I may have just been jipped but my new master cylinder didn't compe with a new pin, so I had to reuse the pin. I dropped it twice trying to drive it back in to place, took me more than half an hour to fish it out from the inner fender below. You might prevent this by using a bit of masking tape to tape the pin to the end of the punch to start it back in to the hole.
If you are losing clutch pedal feel, you may want to try the master cylinder first; for less than $50 its good preventative maintenance anyway if you are still on the original unit, and it might fix your clutch engagement issue at least until you can save up for the clutch you'd like to have and getting put in by the right shop.
As per the starting issue i had above, I must have ended up in a flooded condition, although I don't know how that would be possible with EFI....it cranked right up in the evening when I got home that day.