First of all is good to do a quick characterization of your PCB using a 50 ohms transmission line, having a length comparable to the length of the longest 50 ohms TL in your design. Characterize this TL using the VNA (check for insertion loss, but specially for return loss, that shall be better than –20dB). If the return loss of this TL is not very good you will have problems getting a consistent match.
For calibration you can use also a 50 ohms TL part of your design, attaching to its ends two small FSC connectors.
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In this case you have to calibrate the VNA before using two identical FSC connectors, back to back.
After characterization of the 50 ohms TL, do the match and characterize with VNA and NF meter. First for gain and BW, and second for noise figure. Noise figure match will be slightly different from the gain match. Is possible to lose a little bit of gain, but you will do the compromise to meet both specs.