DS,
There were a few subjects, let me try to help a bit, if I can.
R725/729; Good work identifying this documentation error. This unit’s documentation has a few. Documentation errors do crop up from time to time. Sounds like you are on top of this one. Since the unit was originally working I would always default to the actual “as found” component placement on the PCBs as the correct “version” when discrepancies occur.
Good approach taking lots of pictures as you progress, I do the same.
TR705/TR706 orientation; I’ve looked back and can confirm that in this unit, both of these two transistors are installed EBC, with the Emitter leg “closest to the top edge” of the circuit board. (see photos)
Power supply issues (blown 3A fuse); Yes, you’ll need to resolve this issue(s) before you can reliably work/troubleshoot other sections of the receiver. One thing to note; the design of this receiver incorporated what were called “fusible resistors”. You can search fusible resistors if you need more background. They are denoted with the prefix “FR” in the Yamaha documentation and used throughout the unit but, the power supply board has 4 of them as examples (FR801, 802, 803, 804). I would have them fairly high on the list to check-out.
Dim bulb tester; This is up to you but it gives a couple of very useful advantages, and doesn’t cost a lot. In cases of very high input current the bulb (incandescent) acts like a fuse and interrupts power. Perhaps more importantly, in cases of high, but not overload current levels, the bulb will stay bright after the initial inrush current should have subsided. This gives you a sort of “visible display” of line current going to the unit. There’s lots of info on dim-bulb testers which can be searched.