I had to think about this too when AE came out in arcades and I had to move to stick, so maybe what I came up with will help you.
Default Layout, no PPP or KKK.
LK, LP: Index.
MK, MP: Middle, plink with Index (or Thumb if needed).
HK, HP: Ring, plink with Middle (or Index/Thumb if needed).
Throw: Thumb+Index (Kara-Throw: Middle=MP).
LK Stored: Thumb. (I use thumb only for LK Fuhajin Store, otherwise I use Index for better precision).
LK Stored + anything else: same as when LK is not stored, easy access to everything, focus etc.
MK Stored: Middle.
MK Stored + Throw: Thumb(LK)+Index(LP).
MK Stored + MP/HP/HK: Ring.
If you happen to have MK stored with index, you can still tech throws with thumb+middle but that’s less comfortable. However other buttons are more comfortable to use, and you can plink them. I use both.
HK Stored: Ring.
HK Stored + anything: no difference except HP with Middle.
LK+HK Stored: Thumb(LK) and Ring(HK). You have easy access to everything, including plinks/focus. This usually happens if you decide to hold HK for a long period, you can keep fighting without problem.
LK+MK etc: This only happens when zonning or when going for a free combo so it doesn’t really matter. I like to leave Middle free to AA easily with punch buttons if needed, that means the MK is held with index instead.
I haven’t ran into a situation where I felt I lacked fingers with that config so far.
I decided to start using my thumb for throws or LK store to avoid those rare situations where you lack a finger to tech or can’t reach a button.
Otherwise I use Index for LK for better timing, and it is more comfortable to plink MK~LK with Index than Thumb, for example.
I don’t use pinky, but an alternative to thumb is using you pinky I guess.
Also, if you don’t plan on ever playing on an Arcade cabinet, you can swap punches and kicks, it solves the problem ( Thumb can press all 3 Punches whenever you can’t use your other fingers ).