After getting estimates of $4500 - $5000 to replace the liner (and that's with me removing most of the rock, removing the plants from around the parameter, finishing the edge of the pond when they were done - putting all the rocks back), I decided to see if I could fix the leak issue on my own, without having to replace the liner.
I cut back or removed the plants from round the pond. My brother-in-law came over to help me move the large rock where I knew there was a hole and we raised the liner so that the hole was above the water line. Then I removed all the rock on two sides of the pond and looked for leaks and raised the liner. I found two areas that were low.
Added 3 inches of water to the pond and waited. No water loss! Even with the waterfall running, the level of the pond did not change. Waited for a couple of days and water stayed at the same level.
Put all the rocks back, but decided to not put back the plants around the edge of the pond for now. It looks a little bare, but I am getting use to it. Below is a picture of the pond before the work began, and after.