There are 2 ways to do the output jacks for the speakers. The book calls for two speaker jacks, and the kit provides parts for this. In this scenario, you will need to drill a new hole for the second jack, right near the first one. The existing hole is the one between the 9-pin tube cutout and the 8 pin tube socket cutout. You will also need to drill a hole for the impedance switch, typically to the far side between the 9-pin preamp tube cutout and the outer wall of the chassis.
That said, I only use one output jack, even for the two speakers. I wire the speakers in parallel if I use 2 speakers like the book calls for. It it the exact same as wiring the jacks in parallel (as the book states) and running speaker wire to each speaker individually.
For question 2, it doesn’t really matter, whatever makes sense for you. I do it just as you described.
Three, this goes on the largest flat surface. I usually use one of the predrilled holes and then drill another with the PT at an angle.