Had this 2000 FXDX about a month. The guy I bought it from said he had the dealer flush and bleed the brakes but the front dual disks still felt mushy. I got a rebuild kit for the master and re bled them feels better but the first pull goes almost to the grip. Repetitive pulls increase the distance from the grip that the handle firms up. Pads are within tolerance.so are the disks. 16000 mi on the bike.
Any ideas? I bled the brakes forward and backward. Even removed the master when I back bled it and held it so no air would be trapped at the banjo fitting.

 

Oh yeah it's a 11/16 master

 

And Dot 5

 

you still have air in the lines it sounds like... i would rebleed, did you start with the caliper furthest from the master? then do the other, go back, go back done... may be time for caliper seal rebuild as well

 

The early dual disc Master Cylinders had issues, there was an article on it in american iron, I forgot what issue. Mine is the same way. I'm not sure a rebuild fixes it or not but I got a newer revised one ready to put on mine just gotta get the time and the other bike back together first

 

Probably not the main issue, but those old rubber brake lines can also contribute to spongy brake lever.

 

One of the main causes of this is that these calipers don't "float" like the old style calipers did.
If the caliper is not centered over the disk properly, it'll cause this problem.
I have cured the problem by installing shims in a couple of cases and also by installing floating rotors that center themselves in the caliper.

Measure the distance between the caliper and the rotor on each side of the rotor, if it's off by even a tiny bit....That's probably your problem.

Lots of dealership mechanics don't know how to fix the problem and many don't even recognize it as a problem.

 

I had the same problem on my 05 super glide. Soft to my liking and the brake lever would almost touch the grip.
I got it fixed by accident. I bleed the system with a pump, hand bleed it, reverse filled to no avail. I pulled the front tire to plastic coat the wheel. The brake pads/pistons were really tight Cleaned it good got em moving properly. After installing everything back together. I now have a full front brake. I did bench fill the master cylinder to see if it was working properly. There were no problems with the master cylinder. I mean it is as good as dual disc are.
Its worth a try. I have brakes out the yang yang now.

 

Well I did one more bleed to no avail. Calipers look centered. Going to pull them off next and clean them up. I have to say pumping the handle dosent feelmush like air it's more like pumping up a Jack.

 

If it doesn't work try replacing MC with 45013-96D it is a few revisions newer than the one on your bike, I don't have the issue of American Iron anymore, but it fixed the same issue on a bike they were having an issue with.