I'm not sure if it is excessive. When you monitored it initially, did you approximate or measure exactly for any water loss?

In a pond that large, 3' seems like a lot, but evaporation could account for a lot. Also, do you have animals visiting it that drink from it?

A few months of drought could cause that much loss, but I'm no expert.

When you dug the pond, were the bottom and sides puddled (stamped repeatedly to get rid of any air pockets in the clay, and seal it better)?

the bottom and sides were repeatedly compacted with a large loader, there is no evidence of the local cow population using the watering hole (although I would welcome their soil compacting.)

When I initially monitored the pond the water level was only a few feet, and I did not notice any measurable loss over a weeks period.

Since I have been monitoring the water level closely, it appears that I am losing around 1.25" per day on average. At first I though that evaporation could be the culprit, but the temp has dropped considerably and the loss rate seems to be the same.

Here are two good links about evaporation in the US. In the 2nd link, there is a link to the annual evaporation data for the US (data is old, but probably is not much different than now).

http://www.dynsystem.com/netstorm/docs/NWS34EvapTables.pdf
http://www.grow.arizona.edu/Grow--GrowResources.php?ResourceId=208

I would be looking to see if any of that rock you mentioned is poking through to the surface That can be a big problem. The hose is suspicious as well. It could easily have damaged the packed clay down to loose soil. Clay can absorb a huge amount of water.