Always turn release check off. Will save you from getting off extra inputs. It’s only really useful in very specific circumstances which you will likely not encounter.
I prefer input timing to medium, but different people prefer short. Having it set to long can get back, forward motions accidentally come out when moving in neutral, so in general most people change this.
I would put input shortcuts on. It essentially fuzzies inputs so if you’re completing a move that requires a down, forward motion; a diagonal down+forward, forward motion will work. Generally helpful.
Everything else is personal preference.
I like having button shortcuts on (I sometimes use it for grabs/stance switch/super)
Unless you’re using a fight stick, I don’t recommend using alternate controls. Even then, it makes all motions into circular ones; increasing the execution requirement. It’s good for people who are already used to it, but not something worth learning.
In terms of button positions when I’m using a standard controller, I prefer having block on the front trigger, but that’s personal preference.