Wait, you've replaced the master cylinder and did not bleed the brakes? If that is the case you would have air in the lines.
The procedure is something like this (assuming you have a helper):
Start farthest away from the master cylinder first and move toward it right rear, left rear, right front, left front. You need a chunk of hose that will fit over the end of the bleeder and go down to some container to catch what comes out.
Find the bleeder, it is right near where the line goes into the wheel cylinder.
Get it freed up, also helps to just take out and clean it, blow the crap out with brake cleaner/air/small wire whatever it takes.
Then with the bleeder closed and the hose on it, have your helper pump the brakes a few times, then hold them down. Open the bleeder a bit for a few seconds, close it, tell your helper to let up the pedal and pump again. You should get some brake fluid out. Repeat about 5-10 times, more for the first wheel of each set (front or back).
Every couple of times, check the fluid in the MC resevoirs and top them off if needed. As you do it, you will get a feel for how much it uses up each bleed cycle, so check often at first.
You should start to get some pedal after the first few times. If you can find some clear hose to use it helps, you can see the air coming out and tell when to stop at each wheel.
Repeat for each wheel, moving closer to the MC each time. When you are done you should have gotten a good stream of fluid out of each one, and you should have good pedal height. Replacing the MC will sometimes require quite a bit of bleeding, because the air will have to travel quite a ways.
The book is pretty paranoid, saying you should have the motor running when doing this, and place a board under the pedal so it does not bottom out. On a new MC, the bottoming out thing is not nearly so critical though, and I've never had a problem doing it with the motor off either.
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