Brakes have me baffled!

AdamR said
Hey, what push rod are you using with tha master ? If you have the adapter yo've moved the master out about a 1/2" and are probably trying to pull the push rod out of the back of the master. Theres your clunk and fluid noise. You may need to get the adjustable push rod.

I get the clunk on the down stroke... I was thinking that if it was too short, when I first step on the pedal it's got a longer way to travel before it hits the piston in the master. Does that sound right?