Whew. There is a lot to look at here.

To me, it really comes down to the high primary voltages. I think Id go with the combination that is getting you closest to 330V and let it ride. Some fluctuation is fine. My sense is that you are getting in the weeds with the 5Y3 calculations. This amp is REALLY forgiving. The design can accommodate quite a bit of variance.

It seems like voltages are high throughout and your measurements of the PT confirm that. I think that running it at the 120/300 combination should be fine. The PT might have a bit higher output than specs.