Is there a standout tour company I should use for the day and overnight stuff?
Not that I could say. I booked my day trip to Saqqara pyramids though the Conrad I was staying at and was only just.
@boomy was there just before me IIRC - he may have some ideas. All the rest of my touring was part of larger tour, or on work. Viator probably a good start eg
https://www.viator.com/Cairo/d782-ttd
Unless you are very fond of camels, resist the ride at the pyramids. Takes time that could be used elsewhere.
I think no matter who you book with, it'll be a individual subbie who takes you, so luck of the draw. Make sure that they will take you to ALL the places you want or arranged to see. Confirm at the start, and half way through. Check what's covered in their fee - entrance fees/photo fees etc. I know you've been around a lot, but here its all a bit ... fluid.
Most of Cairo attractions you can do by yourself, via Uber. A guide would be good, but not essential. Most of it is overwhelming, without the detail. Same for Luxor. Valley of the Kings - you have to go across the Nile, then from memory, 30mins on road to the entrance gate. See my TR on the Nile re ticket types/combos. Strictly, you could get there by Uber/'helper' but a tour might be useful for logistics.
Just be prepared for craziness.