I know Tha C-Master was supposed to upload some more neat videos with alternate inputs.
I don't recommend using SF4 to practice on a new controller. The very loose inputs and input storing can really mess up your since of execution in other games. I always recommended Capcom vs SNK 2 for the following reasons:
1. You have training mode, and some older games don't.
2. You can adjust the speed to very slow (1 star) and learn the inputs slowly, and increase the speed as you improve.
3. It doesn't have the input leniency of SF4 or most newer game. You have Kof inputs AND SF inputs and you can learn both.
I think the hitbox is your best bet because you have the quickest speed (especially once you learn alternate inputs), more accuracy, and as you said comfort. I like being able to play all day with no discomfort or being able to lay down and play if I see fit.
One thing you can also do is also do some trials or beat up on the CPU to help yourself mentally do the motions. Doing it in practice is a start, but you also want to be able to react with it. Which also takes some practice.
The jump button being down allows you to use your right thumb to jump, which means you are using two hands to control your character, with one finger on each button. This way you have the quickest and most precise control for things like 360's and tiger knee inputs.