Thanks for the photos! Those voltages do seem a little low to me, as normally the 600Vct. specified for the B+ winding is at the rated current draw while in this case you're getting somewhere closer to 545Vct. at whatever fraction of the total load normal operation is. A good way to check if your PT is operating on spec is to measure the value of the heater voltage (it should be a little bit above 6.3V). If it's really close on that value, I'd probably shoot an e-mail to the folks at Heyboer and ask them if that voltage is right for the iron. I really hope you don't have any shorted turns in the HV secondary from those previous problems
If the B+ you're getting is a normal, expected voltage for that transformer, I wouldn't worry about it too much. I use a bucking transformer setup with my Hammond iron to produce either 385V, 410V or 435V for the B+, and I'm sure that the very subtle differences between the lower two voltages could be tweaked out pretty easily in the circuit if one were so inclined. 385V is great to run 6V6es with too!
Those knobs look fine to me, although I think the real deal are the Davies 1510. I'm really looking forward to those clips!
Matt