Sorry to drag you in to the quagmire. The X-Y plots can get pretty bizarre, especially when distortion from different sources (output stage valves, and especially output stage transformer) impart their own quirkiness.
Can you confirm you have disconnected all the high-freq roll-off circuits that are not of influence - the schematic in your first post shows a 200pF cap shunting the PI output, and you need to short out the grid-stoppers as they are likely an influence with miller capacitance. Also the dominant phase shift is likely to be from the plate resistance of the EL84 (which could be quite high in pentode mode) and the shunt capacitance of each half primary winding (ie. remove the MOV's or add capacitance to see how much of an influence that is).
Can you confirm you have disconnected all the high-freq roll-off circuits that are not of influence - the schematic in your first post shows a 200pF cap shunting the PI output, and you need to short out the grid-stoppers as they are likely an influence with miller capacitance. Also the dominant phase shift is likely to be from the plate resistance of the EL84 (which could be quite high in pentode mode) and the shunt capacitance of each half primary winding (ie. remove the MOV's or add capacitance to see how much of an influence that is).
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