I replaced the batteries of the Busby box today to see if that reduced noise. It did not. Measuring the instrument noise and TP7 noise gave exactly what I got yesterday with the old batteries. I subtracted the instrument noise to plot against the model again and got basically the same graph as yesterday.

I also tried comparing the phase noise coming from the electronic noise against the total noise of the VCO. The total noise of the VCO was apparently below that of the electronic noise. I'm wondering if it could have been the fault of all the ground loops, since removing almost every cable changed the graph of the electronic noise so much. So at some point soon I would like to re-connect the entire VCO and measure the phase noise again, making sure I remove every unnecessary cable. This part confuses me though - all the schematics label the connecting resistor as 0, so I'm not sure if there is a 0 resistor or if it's a value that I don't know?