Personally, knowing what is wrong with my shoulder, why, and how to fix it would be my priority.
Sometimes its as simple as technique; sometimes its not
There are endless recommendations in his books, on the net, this website, his forum, etc.
Google is your friend
People have used floor press and weighted dips in lieu of benching. Plenty of options.
You may also want to look at your assistance exercises. Find the right ones for you. They may alleviate your shoulder issue.
Push Press, Push jerk, Military press, Klokov press can all be used for Main and assistance vertical pressing exercises.
same with front, back, bodybuilder, box, front straps, and zercher).
But I am sure you will get someone that says you are a sinner if you veer from the path and totally disagree with what others have done. Its your path.
If you want to follow the book by the book do the book and all the recommendations Wendler has given. People have had great results with the programs Jim has laid out.
There are so many variations of everything there really is no boredom unless you just get tired of 531 at this weight and that %. It is one of most popular templates with the most flexibility.
However, You dont have to follow the book to do the same rep, set, % scheme.
Do what you want not what someone else says. Nothing is a matter of fact.
If you are not happy doing it then why do it at all.