Well, actually, no, I did do what you are saying, but I am learning due to some of this process anyway.
I found only on the scope test phase, and things seemed odd. At that time it was recommended to me to put a guitar in and put the speaker and see how it sounds.
Before that, I was following all of those steps. i.e. brought up voltage on the variac, found an under specced resistor that started smoking early, then fixed that, brought up the amp again on variac, voltages all seemed stable, added the tubes, seemed stable, hooked up sine wave to the input, and at that point I saw odd behavior.
I was asking at that time what would be best next steps, and was told to plug in a guitar and verify that it is indeed doing so. That's what I did.
There has been a massive amount of back and forth by multiple people all helping. (which is greatly appreciated), But with each one it seems to help me narrow it down a bit further, but also adds to the overall confusion of the thread for others to understand what's been done.
I've just had to repeat some steps a lot to confirm things because this thread has been so hairy and long running. I forget what I did and what I got. (I really need to start keeping a journal with notes on everything so I can go back and say "Yes I did this, and here was the results" etc.
I'm learning a massive amount with it, and am happy this forum exists to teach me this kind of thing, but I know this thread is becoming epically painful for everyone that's trying to help...

~Phil