Here are some thoughts for improving your pull-ups (and for anyone else who may be struggling with this) from my perspective:
1) Give it time. When I did ladders I noticed my pushups jumped up quickly while my pullups only went up by .5 or 1. How long have you tried ladders? I would dedicate about 2 months before trying something different.
2) Don't "modify". S&S, FPP, A+A and LSD are all effective programs and if you deviate you will not find the results you are looking for. It take a lot of patience. If it says "do this nearly everyday" don't drop down to 2 or 3 days a week.
3) Trust the process. We military folks tend to add things to our training. I used to double CrossFit workouts because my body had such a high capacity for pain and endurance. I do the same with StrongFirst. I'll do S&S and then ruck, and MARSOC short card, and.....I would assume you might be doing the same thing. Evaluate your programming and ask yourself "why" a lot. What are your goals? How is each and every workout achieving that goal? If it doesn't achieve the goal or is "extra" cut it out. You may not be getting your pullups because you are doing too many rows, or butterflies in the pool, even too many pushups can fatigue your pullups.