Measuring the bode plot of an op-amp circuit
Based on the transfer function and the circuit, the contents of the red box is a lead lag filter, depending on the choice of C1 and C2. The difference is dependent on which capacitor is larger. For some frequencies, the gain will be will be unity, and for others, it will be C1/C2. Lead/lag filters also have an effect, of course, on the phase. One causes lead for certain frequencies, the other lag. 

You are correct in that the second op amp is a buffer. Most likely the ratio is simply an exercise for you. However, at a certain frequency, an op-amp will begin to act as a low pass filter, although the MCP6022 has a bandwidth of 10MHz. This could mean anything, but I'd expect to see -3dB drop here.

Others may correct me, but I would expect your input to be across JP22. I don't think that the TP41 will tell you much. Your transfer function is certainly from JP22. 

I don't think your numbers mean much without the input? But I would suggest making sure that you're converting from Hz to Rad/s for your transfer function.

Good luck and perservere! Please feel free to correct me, I'm a student also.