When I first did my trooper up with all new brakes and stuff I couldn't get very good pedal travel either and I bled the brakes numerous times.I even took it to a shop and had them bleed the brakes with the same result.When I put the pedal down it was almost to the floor , and even then it had little effect , they were very spongy.I poked around and asked questions on the board and found out about that adjusting rod on the brake booster and I adjusted it.It doesn't take much to adjust it , a couple of turns , and my pedal travel was greatly changed to the point where the brakes came on as soon as the pedal went down a little less than 1/4 way , like they should with all new brake parts.I think if you turn it too much , the rod will stick out too far.

Also , did you bench bleed the new master?That makes a big difference too if its not bled properly.I would lean towards the rod needing adjustment though , especialy seeing you put on a new master.Just give the rod 3-4 turns and give that a try , if its not enough do it in small increments untill you are happy with the pedal travel.