I am not the 1st to respond, but I have used my NanoVNA to tune a 6 cavity Waco VHF and a 4 cavity, "Cigar tube" UHF duplexer (Ritron). Regarding notches When you approach 70db attenuation, the graph gets "noisy".. With a NanoVNA use at least 2 passes per 1Mhz. It's slow but seems to get the job done. Since you can not resolve -90-100dB with the NanoVNA. I opted to "imagine" the dip to continue below a smoothe line in the area of the noisy bottom.
I used a marker on my desired frequencies and tuned so that the marker was midway between the noisy area of the notch.. I hope I am expressing the theory that the "dip" is symmetrical, and "down in the noise". Having the marker frequency set mid-way in the noisy area should "guesstimate" the lowest point of the notch. I did save a snapshot of my start as you can see the notch area is off. The markers are 144.67-145.27...Ideally you want the marker in the middle of the notch noisy area..Not everyone is rich nor has access to expensive commercial test gear. 40 years ago I watched a guy tune duplexers with an 10 watt transmitter, a receiver. a VTVM, 140 feet of RG-58 coax and a step attenuator. He made the duplexers out of old soda water fire extinguishers.