So far, I think I managed to place the cleat in a good position for my foot. I no longer have hot spot (yay!) and numbness. I only did short rides of 20km although. I can feel a small inconfort in my knee however and I believe that the cleat orientation might need to be adjusted. Is the best way is to look how I pedal in a mirror?

The best way is with a fitter, measuring the knee angles. Adjusting fore/aft will affect the knee angles slightly, and heel in/out will affect the knee tracking. Then there's Q spacing. Don't forget custom insoles/wedge inserts for pronation, etc... too. There's kind of a lot to this.

I paid $$$ for a good fit, and now almost all of my problems are gone just a few weeks later.

Surprisingly, what felt good at the foot (more heel in towards the chain stays), was not what was best for my knees.

Ask a buddy to follow you when you are riding on various terrain (flats, uphill, sprints, etc) and watch your knees from behind. If your knees track pretty straight up and down without wobbling or twisting as you pedal, then you're in really good shape. Some people will need to pay $$$ to fix problems in their pedal stroke that could cause knee injuries down the road. A lot of people are happy with just pointing their cleats straight ahead and aligning their knees with the pedal axles.

What did you end up doing?

Well, I paid the fitter, that's what I did. He fiddled with things and now the pain is on the way out.

On that foot there are: custom insoles, a varus wedge, Q spacers, 5mm lower seat height, and the shoe feels a more heel out than I would have expected. Then there's back position and heel elevation changes suggested, along with yoga/stretching for the hamstrings.

All of this has stabilized the knee tracking, which is what I really need for now. Like I said, there's a lot to this stuff. A good fit is pretty awesome.