Keep chipping away at the Squats along with the deload procedure. You get 3 attempts at a weight at 5x5 (remember even if you fail before the 5th set, attempt all 5 sets), then deload by 10% and work your way back up. It's natural not being able to lift your 5x5 max in any exercise 3x/week.
How much weight have you been adding to deadlifts? When I started I'm sure it said add 5kg(10lbs), rather than the 5lbs in the rest of the exercises. Stick to the 1x5 and keep adding weight, there is no need to feel that you have to burn yourself out every workout.
Be careful with adding incline and the possibility it could tire you out for your main bench. It's very easy to add extra exercises at the start and not feel an effect, but when the weight catches up with you you could find yourself in trouble. It's not just your tris/chest, your shoulders will be hit as well and you don't want them fucked when you're pressing 2 days later.
I don't recommend adding weight to inverted rows. Are you doing the feet elevated version, or are your heels on the floor? Keep at it, your numbers will start going up. When you hit 15, switch to the feet elevated version (if you aren't already) and when you can do 15 switch to barbell rows 5x5 (or 3x5). That's when you start adding weight.
I'm surprised you can do more pullups than chins, it's usually the other way about. The truth is you're adding weight to these every week without realising it - body weight! So you are getting stronger at these, if you were to lose bodyfat and keep your muscle the numbers would go up. Also these are a tough exercise to add weight to. After your 3xF, do 10 negatives, as slow as possible (instead of rows, leave this for Workout A). If you're thinking your lats aren't getting enough work, use wide grip.
Although overhead press is the first to stall and hardest to add weight to, I'm gonna guess that the amount of exercises you've added is tiring your shoulders out, and adding to it. They're small muscles that need rest. Again, your upright rows you're doing for traps are gonna tire them out. If you're worried about your traps, shrug during deadlifts, and make sure you shrug up at the end of every overhead press rep - it's your traps that are holding the weight in place if you do it right.
Can you do 15 good pushups in a row yet? If not, stick to 3xF. If you can, do dips 3xF. When you can do 15 in the first set, switched to 3x5 weighted dips. The idea in all these exercises in stronglifts are to get you strong, not to get you a good "pump".
You just need to be patient with it man. There's a good chance when you add extra exercises you won't give the targetted muscles a chance to recover and grow (and even beat up other muscles that the exercise doesn't target). You're close to pushing your 5x5 max in all exercises, and the rest to failure. Squatting heavy 3x a week. The stress it already puts on your body is high, don't overwork and keep it simple!
If you're keen to do extra, there's plenty you can do - dyanmic stretches (or anything that improves your flexibility. good for injury prevention), foam rolling, grip work.
But during your stronglifts workouts, try to stick to the program and the deload procedure. Just because you don't wake up sore or get a pump doesn't mean you're not growing. I barely got either but it didn't stunt my growth!
Hope this helps man
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