I will try to give my 2 cents to it: A big part for me is to have a consistent setup (how am I holding my mouse, how am I sitting, how am I moving my hand) to be able to create muscle memory, which gives the best results for me. Then there is figuring out how much force you need for a perfect hit, which varies when you buy the Hammer Upgrades. The amount of force required sinks significantly, at max Hammer you need about as much Force as when tapping a Glass Nail in the beginning, maybe a little more. You are right, the most important thing for speed is to get perfect Nails and as many of them in a row as possible, because the Multiplicator is the biggest factor, which you buff with the Plank Upgrade. The Nail upgrade seems to play into the Multiplicator aswell, but I am not sure by how much, still working at that.

Outside of holding your combo, you can get quite a bunch of money just through the Hammer upgrades, at max Hammer Rank you get about 3k$ per perfect hit, it quickly adds up. The Hand Upgrade is not as important in my opinion. Upgrading it results in you being able to hit the Nail a little deeper, potentially reducing the amount of total hits required. You notice this the most with no Hand upgrades, you need quite a lot of okay hits, upgrading reduces that. Only at the max Hand Upgrade you are able to get a Perfect Nail in 2 Hits, anything outside of that I feel makes it harder to achieve 3 perfect Hits, since then the Nail is way lower and it gets easier to hit the Hand or the Plank, killing your Combo.

I wouldn't bother with the Bug or Passive Money upgrades, for example Deck 1: with all perfect hits, full combo, you can get bit more than 4k$, while one bug gives you 10$, which is peanuts in that case. But if you struggle with getting more than 200$, and hitting 3 bugs, suddenly you could get enough money for 1 nail, 1 plank or hammer, which makes it easier for you to jumpstart your run.

Will there be a Discord Channel for Theory crafting? I am currently modelling the game upgrades / money progression and I'd be happy to share once it's finished.