The motor mount mods made all the diference in the world. The runtime is now about the same as the stock setup. Ironicly, after testing a few different props, with the motor lifted so high, it runs best with the stock prop.
The reason for the handling problems is that in order to acheive maximum lift and minimal drag, the thrust angle and motor hight force the boat out of the water on takeoff. As for handling at speed, I think it has alot to do with the fact that the boat it not build to go fast.