One of the best tools I have purchased lately is this brake bleeder.
http://cgi.ebay.com/ebaymotors/Vacul...spagenameZWD1V
I was having a hard time bleeding the clutch master cylinder on my 32 Ford. Air bubbles don't like to go downhill. This thing got it done in about 15 seconds. You simply add a hose from the bleeder to the bleed screw and turn it on and make sure you don't run the master cylinder dry. It pulls fluid thru the system fast enough to bring the air bubbles with it. No mess either. You need a air compressor to power it though.
Yes if you step on the pedal witth the master cylinder unbolted from the booster you should see the rod move that is sticking out of the booster. Check the length of the rod also and make sure when the master is bolted back up tat the rod almost bottoms out in the master. If the rod does all it's moving before it contacts anything in the master you have a problem.