[Marsupial]

That power transformer looks great to me. the one on my 47-1230 (sister model to your 46-1209, almost identical) is very, very similar & works like a champ. These are pricey, don't change it unless required to.
The output transformer looks like it was burnt. I'd still test for continuity. Do you have a multimeter?

Have you done basic recap yet or is it still running all the old caps? Don't power it without the speaker, the power circuit include its coil. I'd work on the capacitors before doing anything more. If there's a fault in the circuitry causing the output transformer to burn, changing the OT might only result in more flames.

BTW as long as the phono button is stuck, you'll never receive any signal. The good news is that you can connect about anything trough the phono input, its a rather standard mono input compatible with almost anything. I ran an MP3 player and a computer trough mine, best way to test the amp recap.