I'll be darned... I would have expected a rotor warped enough to require the lever to be pumped would have made the brakes pulse, as you said earlier. I hope this does the trick for you.
As long as you're planning to remove them anyway, you could try straightening the warped one. A forum member recently posted that it is actually very easy to do with nothing more than a crescent wrench and an indicator with .001" increments. You mount the indicator to a stationary part of the bike, set the indicator against the rotor and slowly rotate your wheel to find the high or low spot. Using the wrench as your lever, you pull or push that spot into line with the rest of the rotor. He said it takes surprisingly little effort to bend the rotor. Might be worth a try. If nothing else, you'll know how easily a stock rotor can be warped.

Good luck!

 

I'm getting in here a little late and it seems like you have found your problem.
For future reference, with your bike sitting still you can pump your brake and hold heavy pressure on the lever. If the master cylinder is bypassing fluid, the lever will slowly move to the grip. If it doesn't move past the original pumped up point then it's not bypassing and you need to look elsewhere.

 

Yeah I am surprised they didn't even try to spin the rotor. $60 down the drain and it would of been another $600 in parts and labor for the new lines and master cylinder. Either they just overlooked it or they wanted to get some easy money.

I ordered a rebuild kit that should be in by the beginning of next week. I'll be installing the Street Glide rotors this Friday if they make it in that soon but I'll still use the extra parts I'm getting in.

Yeah it was a big surprise to me as well. I could see where the rotor completely lost contact with the pad and the small movement of the pistons is actually what caught my eye. I'm going to check my brake pad and make sure it's still flat as well but I may try to bend the rotor back and sell it with the original wheel/tire.

Good info for anyone else who has this problem. It was one thing I noticed initially when they said it was the master cylinder. It had to be pumped but it stayed very firm while slowing down.




I'm happy it's all (hopefully) figured out. I got some used rotors to put on and then the new shiny ones get to go on later. A bent rotor was the last thing I expected to see but I'm surprised it wasn't the first given how bad it looks when you try to keep an eye on it.

 

Hey I can stop now! Plus they look pretty nice.

 

Well thanks to this forum, I finally found the problem. My front brake was soft/spongy pull and required increasing pressure to hold at a stop. The brakes would work but the initial pull didn't provide much braking. After replacing pads there wasn't much difference (some). I took a suggestion from the forum and pulled the calipers off, placed a thin metal bar between the pads and pumped the brakes. Suddenly the cylinders moved out about 1/4 inch and I was able to spray brake cleaner on the cylinders and brush them with a tooth brush where I could. Put them all back on the bike and WOW, the brakes are firm and requires two fingers to activate. They are working as they should and provide a nice firm, smooth stop. Thanks guys!