The clutch master is a pump, similar in function to the pump on a spray bottle. In order for it to take fluid in to pump that rod has to allow the cylinder plunger to come all the way to the top. Should be about 1/8" play between that rod and piston with the pedal released. Same for the brake master. When the trans was out did you remove the clutch pressure plate and disc? A busted disc, springs, etc. can also do this. 

-----Original Message-----
From: Vanagon Mailing List [mailto:vanagon@gerry.vanagon.com] On Behalf Of thewestyman
Sent: Wednesday, May 14, 2014 7:30 PM
To: vanagon@GERRY.VANAGON.COM
Subject: Clutch can only go half way ...

Hi to the List,

The clutch only can go halfway and I can’t find out why.  It does not disengage yet.  
Adjusted the master down as much as it goes.  Put new master, new slave, blown the hydraulic line out.  Took the transmission out to see if there is anything in the clutch area, but found nothing wrong.  
Am I missing something?
Zoltan