Yea,
My contractor knows ... its been a pain and will continue until completion with how wet it is. He has a 12-14 foot spot dug out that he has been pumping out water while he has been taking away soil from the other area of the pond. I suppose at this point I will just have to wait until the entire pond is dug out and we can take a look at where any potential water is coming in before deciding which options might be best.
I have my contractor working on a quote now to haul in / put the clay down. I also received a few liner quotes back from various companies and it seems like a liner would be the cheaper option at this point. My biggest fear is the bubbling effect it can have. The companies I have received quotes from haven't been to helpful on advice with the situation... they just sell the plastic I'm told haha.