Tough decisions ahead for you BigPond.

Just my two cents worth. If it was me, I would do some ground work/sealing first. Reason being is that your pond is close to empty, so that makes it like starting all over. Why fill it up now (at a monthly cost ), drain it and do work later to seal it. I agree with them above that you want a good water source, and you know now that runoff isn't enough. So I think you will need to do the pump anyway. I personally don't like the idea of needlessly losing water when you are paying for it.

BigPond, Is the current water level stabilized? And if so, is there a place around that water's edge that looks like it is seeping? Have you been able to get anybody there to look at the situation?