I have quite some experience with this template, it works great as is and that's how I used it. After the main lifts there really isn't much assistance not really much more than most templates. You can complete this in under an hour. You can superset where its practical and makes sense and remember that assistance should not take a life of its own.
I began using this template with my son when he was in highschool and I still use it as part of our yearly plan depending upon where we are in the year.
You mentioned perhaps 5/3/1-ing the incline press, if you did I would make either the bench or press an assistance lift and not run all three as 5/3/1 during the same week. Or you could replace the bench with incline for a number of cycles instead if you wanted to focus on driving up your incline press.
As for swapping the incline day to Friday and moving the press to Wednesday, in the grand scheme of things you have a slot for a "press" on each day so you are just swapping one press day for another press day within the same week, so don't split hairs since both are programmed. If you put the press on Wednesday use it as an assistance lift because you don't want to have 3 heavy 5/3/1 lifts in the same session. Which means yes you could try incline bench on Friday using 5/3/1 and see how it works for you.
Just fyi, but from an efficiency standpoint in the weight room I prefer the pairing of the front squat with the press as its more convenient going from one to the other especially if in a busy gym.
Just my 2 cents, my advice run it as is, but if you really want to focus on incline for awhile make the changes and go for it. Goodluck!