Rember don't push the master to far or it can ruin the master only about 1/4" travel is all you need.
But now that you have it on the jeep you may have to power bleed the system to get all the air out.
Pumping usually means air in the system, that is if they pump up and are fine, if they are soft all the time and don't really pump up you may have a different problem. I have read alot on the discusion about one ton masters and the such. I have one ton axles on a blazer and still using the half ton master and booster, they work well. I had to bleed my brakes about a billion times ( no serious i counted) even after bench bleeding the master. They work well now.
I did not change the master out just a couple of lines, But it does have better feel after one pump. So I will start bleeding them some more.Makes sense that it could be air. It just seemed strange that I have already dumped about 3 quarts of brake fluid through the lines already. Im learning ! thanks mike