First of all are you getting a rough idle when it's idling becuase the booster has a hole in the diaphram? If you are not getting a rough idle, there is a seal and tubing that goes from the booster to the intake manifold. Check all of that to make sure or just trade those portions from the other car that you have and see if that works. The point of your pedal going so deep makes me wonder if your master brake cylinder needs to be rebuilt. If so that's not too bad of a job and something to consider. Have you checked the brake cylinders on each wheel to make sure you don't have any leaks, that should be a given.

Hope that helps.

Bill