Slowmow,
First you need to change barke fluid as well, just in case i make the comments.
To your first question, base on my experience you have uneven brake pad material deposit on the rotor. very well descripted problem in many blogs.
Solution in my case, I change pads and rotors at the same time (OEM rotors are cheap), if not you can sand them before the bedding process.
Here you have more info on that topic.
Can not help on 2) and 3)
https://www.apcautotech.com/getmedia...c-8-2018_1.pdf