Hello again,
Little update...
I have found that one of the main problems is the Arduino connectors and the little plug boards that are often used for prototyping. The connection to the plugboard is somewhat variable, so that the reference voltage and/or ground can be changing by as much as 80mv, which is a lot for an analog project. This means the reading will always vary.
To test, i used a 3 point, 4 digit calibration scheme with a second order fit, then compared readings. The readings match one time, then dont match another time. If the power is turned off and then back on, it might read as much as 10mv difference. If the wires are just moved slightly, it might read 20mv difference. Calibrating a second time shows the same behavior, so the main problem is the connections between the 328 chip and the power supply ground and/or +5v line.
So the lesson here is that the plugboards are not any good for serious analog as well as high frequency projects. This little project will have to be all soldered together for better repeatability and proper testing.
An interesting point here is that the plugboard circuit draws very little total current, yet the connections to that board are still important. For example, the filter draws less than 1ma. You would think that would not form much of a voltage drop because even in 1 ohm (which would be high for a short wire and connection) it would only drop 1mv.