Re: 5/3/1 without bench
To answer your initial question: keep the bench press in the program. Generally speaking, when you decide to follow a program...follow it. As you become older and more experienced with working out, you will learn which exercises work best for you and which ones you can omit/substitute. Until that time, it's almost always best to follow a reputable program like 5/3/1 or SS to a "T."
But, I have to ask: have you considered Starting Strength? You're 16, exactly the kind of person Rip designed SS for. 5/3/1 is a great program but with someone your age, I would rather see you put in way more volume on the big lifts to 1) take advantage of your recoverability and put on more mass and 2) get more quality repetitions under load to help reenforce the proper movement patterns.
I've used both SS and 5/3/1 and definitely see better success with beginners with SS. This isn't to say that 5/3/1 doesn't work, only that I personnally feel that it is a little too convoluted for a beginner to wrap their head around. Also, setting a PR 3 days per week in the gym is a great way to keep someone motivated.
If I was in your shoes, I would do SS through 2 or 3 resets and then if you still want to continue strength training, switch to something like 5/3/1 or westside-esque training.
Either way, find what you enjoy doing and be happy that you have "found the light" so early and are doing the right stuff in the gym instead of using machines like most of us did in HS while "strength training" for our sports.