After some fiddling I now have a decent amount of signal coming down from QO100, but also questions. The azimuth was already correct and I had adjusted that to maximum signal strength on a TV channel with a GT Media V8 Finder. But the elevation is numerically wrong, or the markings on the dish are wrong, which is more likely. Fiddling with elevation got the strongest beacon signal at about 26db and 26 degrees marked, but the AMSAT info says it should be around 23 degrees at my QTH. Mind you, for all I know the garage wall is not perfectly vertical! All SSB signals look good now except for one or two that are difficult to hear.
However, having got that far, no adjustment to the position of the POTY in the arm or its skew make any noticeable difference, so I’ve left that one.
Also, when transmitting a tone from SDR Console it actually peaks higher than the beacon so I had to reduce the drive appropriately. An SSB signal test showed very poor audio and no adjustments in SDR Console got it to where it needed to be. Turning the mic gain up in Windows itself cured that and gives me a decent looking envelope when viewing the returned signal in SDR Console.
I just need to force myself to take it all to bits again and sort out the GPSDO input to the Pluto…