Make sure that your MA training falls on a 'run' day, and dependant on how your energy levels are, either do both, or replace one of the runs with the MA session.
With the pull ups, ditch the barbell rows, and replace them with pull ups on squat day.
Negatives probably arent the best answer. Your pull ups are effectively a 2 rep max, thats ok, but it will take time to increase volume.
Instead of doing 2 reps 'all out' every set, you need to approach pull ups in the same way as you would your 5x5 training.
so, sets 1-4, start by doing just one, full, perfect pull up. Thats it, 4 sets = 4 reps, but they are absolute perfect quality. set 5, do your 2 reps.
When that 2nd rep on the last set is as crisp and perfect as the 1st, you can add a second rep to the 4th set, so it becomes, 1,1,1,2,2. When all 2 rep sets are perfect, it becomes 1,1,2,2,2, so on and so forth, then you work through 2,2,2,2,3 then eventually 3,3,3,3,4, and on and on. Its slow, methodical, but it will work, and more importantly, you will be doing proper pull ups, not half reps, kip-ups, or any other weird cheating movement that people count as chin/pull ups.