If you got the same kit I did, the instructions SUCKED. We're talking Ross Perot's "giant sucking sound" sucked.
They forgot one major point: when converting to power brakes, you need to drill a new hole on the brake pedal's arm, approximately 3/4-to-1 inch lower (toward the pedal pad) than the existing hole for the rod. It effectively changes the pedal stroke/ratio.
That should take care of the excess travel.
There should also be an adjustment sleeve for the threaded rod.
Your sig says you have a '63 Suburban, but if you're talking about a hydraulic clutch, if it's factory it's '62 and old (which is what mine is). If you're dealing with a factory-type unit, when you look under the dash, remember that the brake pedal's rod is NOT the one you can easily see from the passenger side. It's buried up/behind the whole pedal assembly. I thought I was adjusting my brake pedal rod once, and then realized I hadn't touched it and had only re-adjusted the clutch rod. The brake pedal rod had loosened all the way, and put the pedal on the floor to stop.
-Brad