Exercise selection looks appropriate. It suspect that you havent done it for long enough, and havent gained enough muscular weight.
5 pounds seems reasonable in that time frame, but remember that that is 5 pounds of TOTAL weight (muscle, fat, water, glycogen) so its not entirely muscle, and that it is 5 pounds spread across your entire body, with the majority going to your legs/back on that program. Shoulders are an inherently small muscle group, so adding noticeable size to them is going to take a while.
Also, 5/3/1 is more strength focused than hypertrophy. Of course it will increase size to a degree, but that is not the focus of the program. Trust in the 5/3/1 program 100% to achieve your strength goals, then maybe switch to a higher volume program at that point to increase the size a bit more. To blend both you might look up “5/3/1 and Body Building” and give that a shot. Again though, its going to take a while to see a lot of size gain on the medial delts.