Tighe: Thanks for the great suggestions!!
I have found it necessary to have an experienced driver back up the pontoon gently into the wind while the kite is in the water to keep lines, board, kites and humans in front of the boat. Otherwise the many sharp edges of the boat will take their toll. The huge wind profile of a pontoon makes anchoring a hit and miss endeavor, and an uncontrolled boat will quickly pass over everything downwind of it.
I finally have a technique for rigging onshore and drift launching off the front that is pretty reliable, and it works well to keep the kite attached to the boat until its overhead and behaving itself!
I haven't used the pick-up line yet; its still in the development stage!

I think it might work well to have two clips on the line, one on the end and the second about 10' back from the end. You first clip your flagging line on the one 10' back, then attach the chicken loop to the one on the end. That should make the kite behave and keep line tangling to a minimum. Swim back to the boat and pull it all in. I don't see anyway around having to rerig onshore, short of handing the bar directly to someone on the boat (try that!!).
Bill:
I really can't see going this alone, a partner to control the boat is necessary. Someone stays on the boat unless you find a nice big sand bar to safely secure the boat and you can play around in shallow water, and someone is a good enough kiter to get back to the boat!
As for the kite, after rigging and folding it carefully onshore, and keeping the bar to kite orientation consistent, I lay the kite inside the pontoon boat and lay an extra mushroom anchor on it to keep it secure while motoring out. Then, when ready to inflate, back the boat gently into the wind, lay the kite leading edge upwind on the front platform of the boat, and pump away. Then place the kite leading edge down in the water, attach chicken loop and flagging line independently to the boat, and unwrap the lines as you let the kite drift away leading edge forward and slightly sideways to the wind. This is where the meticulous line wrapping around the bar pays off.
Eric