Sound on the video could be related to the second problem, where rods are not parallel and perpendicular.
That sound usually comes when they are not parallel so you would need to release pulleys, make sure that you can move axis freely and then tighten everything.
I had the same problem and had the same sound as you do. You need to make sure that when you move head by hand it will move easily to the end where endstops are, and when they do tighten everything and test again
If you set the distance between the two clamps exactly as written in the manual, chances are that the movement is only OK in the center and difficult near the end of the axis. I think most users enlarged the distance between the clamps by a few tenth of a mm so that the axis move smoothly along the full axis.
This is really, really important for a proper functioning printer in the end!
I removed the print head completely and first figured out the best distance between the clamps after which I put everything back together with those newly found distances.
Then, I aligned the x and y axis to the steel rods, not to the plastic housing.
When I got it about right and was able to start some prints, I immediately printed these guides to fine tune the alignment: thingiverse.com/thing:606083
I have the same problem. The bad noise starts when going close to the rear end and the AUTO HOME function makes it make a lot of noise too. The end stop works because it stops at the end stop. Tomorrow, I am going to try to change the distances from the 298mm rod and the 289mm rod and I hope it will work smoothly!
Indeed! It took me half an hour to change the distances a bit so the X and Y-axis are moving smoothly and now everything runs perfectly and the irritating sound has gone.