Miata clutch help

I could use some help diagnosing a problem I'm having with my Miata (2002 with the 5 speed). I put an FM stage 1 happy meal (new clutch, 10lb flywheel, all new bearings) in almost exactly 400 miles ago. I also installed a shifter rebuild kit and replaced the transmission fluid with Ford motor craft full synthetic at the same time. I adjusted the clutch pedal/pin per the FM instructions, and it initially drove great. After maybe 200 miles it started to shift rough. I adjusted the clutch/pin out a little further, and it drove great again for a while. Then it started to shift rough again, which is now bad enough that it won't shift at all. The car will move with the clutch pedal on the floor if it is started in gear, so it clearly isn't releasing all the way. 
 

I thought that even though the hydraulics were fairly recent, maybe I had a bad replacement part and the stiffer clutch did it in. So I just replaced the clutch master and slave cylinders (purchased from FM this time so I knew I was getting quality parts). The fluid was surprisingly gross, so I was somewhat encourage that was the problem, but unfortunately it wasn't. The clutch is also currently adjusted as far out as it can go, the pin is only threaded about half way into the nut in the pedal.

I figure the next step is the pull the transmission back off and take a look, but I'm struggling to picture in my head what could slowly work it's way out to cause the clutch to not disengage all of the way. Does anyone have any thoughts on what could cause this? Any other suggestions before bitting the bullet and pulling the transmission?
 

I wonder if you've got a bad spring in the pressure plate? I'd recommend you call our tech support team, they've got more experience (collectively) than I do with the clutches. 

One thing to check is that you haven't taken out too much free play. Does it change behavior between a cold and warm car?

The clutch pedal pushrod should be loose with the pedal all the way up.  I like to shoot for just barely being able to rattle it around.

Your symptoms and adjustment description sound like you have the pushrod way too long, so the piston never is able to uncover the fluid transfer port at the start of its travel.  When this occurs, the fluid volume is fixed except for the small amount that seeps past the seal in normal use, and it can never get refilled so to speak.

The FM clutch requires minimum amounts of free play - it trades travel for effort. Most problems come from experienced techs who know how they "should" be adjusted. 

If there's not enough free play (and the fill hole is covered), the symptom is usually full disengagement but a clutch that starts to slip as the fluid heats up. The check is to see if you can press the slave cylinder pushrod into the slave. If so, you have enough free play. 

Having it work and then cease to work sounds like something going on in the bellhousing.