[Arran]

Ron;
  Did you power the set up with the shorted 6X5 installed? Was that 6X5 in the set when you got it or was it a replacement you already had? Since this was a high hour set, and obviously the victim of a lightning strike on the antenna coil primary, the power transformer may have already been damaged. I would conduct a resistance check on the two legs of the H.V secondary winding, and a resistance check on the primary, shorted turns on either would cause it to heat up and smoke. This is something I usually do before I even begin work on an old radio, along with all of the other transformers and coils, let's just say I didn't used to and got burned.
 I found a note in my 1937 Sylvania manual that recommends fusing one leg of the transformer primary in any set that uses a rectifier with an indirectly heated cathode, specifically a 5Z4 or a type #84 but it would also apply to the #84's octal cousin as well. Most of the transformer problems I've encountered were in sets from the 1940-42, and they were in sets that used 5Y4Gs, not 6X5s of any sort, the last one being a CGE KL-500. I think maybe it's just a pitfall of immediate pre war radios, maybe they were trying to cut back on materials, less insulation, thinner gauge wire to save on copper, who knows? I have noticed that most companies reduced the size of their power transformers in that era, then went in the reverse direction after the war. We all know about the failure prone output transformers in 1939-42 Philcos which may or may not be related. 
Regards
Arran