Way to power through.
You definitely look as though you will benefit from the stretching. Especially the hipflexors.
Depthwise it looks as if you are a little bit higher than you were before but you're breaking parallel I think all of the time. You are not caving over at the bottom like you were in the first vid and it's like night and day between then and now. I think slowing down the descent a bit helped also.
I see you brought your hands in. But you still have your elbows pushed out way behind your body. Way farther back then most people do or CAN do. You obviously have a lot of range of motion there.
I didn't realize this before but now is see that you are gripping the bar with the meat of your palms. Basically pushing against it with the hard part of your hands with a hard wrist. You don't need to do that. Grip it higher in the hand so you can allow your wrists to relax more. Take some of the pressure off the post shoulder and allow you to relax the elbows forward more. Realize when I say things like forward or backwards I'm speaking in relative terms.
All of this will help your shoulder and neck to relax.
What is the problem you are having at the beginning of the descent? There is always this little hesitation or stutter. It almost looks like you begin to break at the knees, stop, then bring the hips back. Something you are thinking about or are uncomfortable about.
Right now it would be a good idea, on squats, to use you dynamic day, to focus on quality. I'm not saying go slow but have the priority focus more on form issues and smooth motion rather than solely on speed. It is always good to have some "quality" days. You even could up the weights more while keeping the reps low, as it would do you more good to work on these issues with a weight that requires more technique yet is not so heavy that your best form isn't easily achievable. "Heavy volume" day really isn't the best environment to fix things. That's heavy stuff you're pushing so we have to recognize that heavy and best form aren't synonomous.
Trust me, it is not going to hurt you at all to not go for a pr or for de or anything like that, and you can still work up to some fairly heavy weights. IMHO, one of the biggest drawbacks of 5x5's in general is the focus on volume to the detriment of other things like quality and balance. The reason I'm suggesting that day rather than recovery day is because you kinda need more that 8 reps
Work to achieve a smooth, all in one motion descent. Yes, descent matters as much as anything. Each time you move, stop, stutter, etc..your body has to sublety repositioning itself in space and that affects what happens subsequently.
I don't think there is too much that you can't easily work out that way. Basically the biggest thing is to get some of the stress of the shoulders which will basically allow you to get your whole body tighter and more controlled.