It is looking to me that the problem is with the CVR or its wiring back to common.
At 1.6882 MHz and using the 2.2n cap, you are reporting a phase difference of 82.7°. The theoretical phase difference is about 65°, and that makes all the difference in the world; cos(82.7)=0.127, cos(65)=0.422.
How could the phase be off that much? It turns out very easy. In my sim all that was needed for parasitic inductance between the CVR probe and common was 28nH, and the phase changed to 82.7°. Wire has an inductance of about 20nH per inch, so 28nH represents about 1.4 inches of connecting wire.
Interestingly, a parasitic inductance of 100nH in any other leg of the circuit has little effect on this phase angle. Why is that you ask? Well, at 1.6882MHz, the reactance of 28nH is a significant result (30%) relative to the value of the CVR; XL=0.3R compared to the 1R CVR.
How can we overcome this problem? I would suggest using the CVR low-side as the common point for the circuit; that is, right as close to the CVR body as possible. If this is already being done, then it may be the CVR itself that is exhibiting the 28nH inductance. That is where I would be starting to look for the problem.
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