In a similar boat. I quickly remapped the Mac keyboard to work as close as possible to a Win one, and it helped. But it's a leaky abstraction. And now, as some of the modifier keys are swapped, it's always confusing when I see a shortcut in a menu, never sure what to press. So I'm using fewer shortcuts than on a Win. So, for those who are 100% transitioning to Mac, my suggestion is to bite the bullet and adopt the Mac way. But for those who still live in both worlds (like me), I don't have a good answer, just that it's a constant struggle even after few years.
I tried to keep the keys mostly the same but the one I could never get used to was command + c/v/f/etc. It's just too awkward a combo for fingers. Using pinky for control on the left was much better ergonomics. So I swapped control and command keys.