Dwight, See below: (thoughts)
Total pond loop length including feeder lines: 2500 feet
Water temperature in the loop location: 52 F degrees (in Nov)
Area heated/cooled approximately: 2500 square feet living
Ceiling height: 90 feet (with two rooms with cathedral ceilings (18')
Ceiling insulation on average: R38 rating (batting)
Wall insulation on average: R30 rating (batting)(3/4 brick home/siding sitting on a hill with no wind breakers) Exterior walls are 6".
Tightness: (on a scale on 1-5) 4
I am going on the assumption that your ceiling height is 9 feet, not 90 feet.
All of those specifications tell me that all is well in your design and implementation.
Something must be amiss elsewhere. Without actually observing your system in operation I suspect: One or both of your circulation pumps are bad, otherwise not operating properly or there could be a blockage somewhere in either or both sides. One of your compressor stages is not functional or is functioning at a very low level or both of them are functioning out of spec.
I personally would have someone come and test the system, possibly a 3rd party if your heating contractor says everything is good.
I am no expert on the inner workings of a Geothermal system, though I do enjoy a good old fashioned troubleshoot.
