Most likely the master cylinder is ok. Mine squeaked too and worked just fine.
To get all the air out of the line you have to disconnect the quick connect and remove the master cylinder from the firewall, along with the reservoir. I just went through this. Went through 1/2 gallon of brake fluid doing so until I found out my problem.
To remove the master cylinder you have to pry the rod off of the clutch pedal inside the truck. You'll probably have to get on your back with a light and look up. All you need is a flat screwdriver to pry it off. Then remove that sensor from the bottom of the shaft right where it comes through the firewall. That's the tricky part. Remove that white clip on the side of the sensor. There's also a tab on the bottom that hooks onto a metal loop, I snapped mine off. That tab was a pain in the ass.
After that, under the hood underneath the brake booster you'll see where the master mounts at a 45 degree angle on the firewall. It'll either twist 1/8 turn out or unbolt from the firewall, then detach the reservoir and work the pressure line out. This is much easier if you remove the splash guard in the drivers side wheel well. That also happens to be a pain in the ass but I'd suggest it as you might have to remove and install the master more then once if you don't get all of the air out.
Also might be worth it to check out their other videos on youtube. You can see their channel from that link.
Good luck.
Follow this video step by step. It will take care of the air in the line if done correctly.
http://www.youtube.com/watch?v=HgNTDGwcjZc
