I know what you mean with a "on again - off again" shoulder irritation. It's common, more than one thinks in the professional leagues.
Boxing in itself is a very demanding test of physical and mental metal. The workouts are, and can be, grueling. This is especially true with endurance and stamina.
Training with a qualified trainer in that sport would be like night and day, compared to, training with a pitching coach/physical conditioning coach and so on. Two entirely different approaches to two entirely different objectives to shoot for.
If you enjoy the pugilist life style and the commands and demands of heavy physical contact and all that that entails, go for it. On the other hand, working with a boxing trainer won't do much for your pitching game and your shoulder situation. I've had pitchers who have entertained boxing during the winter months because of past persuasions - golden gloves, neighborhood clubs, and the like when they were younger. Some of those guys stayed in awesome shape, others came back like they played kick-the-can all winter ... they were the can!
To be more direct to your question - just be careful of heavy loads and stress demands on that shoulder problem. In fact, a better diagnostic of why you have a recurring shoulder problem would be a good start to monitoring it and dealing with it in a special way, instead of testing the waters with a self-designed program of your own.