Yeh ok , it doesn't sound like a big problem. May be the brake pad scraping on the disc as you say.
Re wheel alignment, I read a few different forums on the topic and some riders use a string alignment taken off the front wheel and use this alignment to check the rear wheel by running the string down the side of the bike either side of the rear wheel to get the correct alignment. I tried that method but I noticed in my case the marks on the rear swing arms are pretty spot on, so that makes the rear wheel alignment easy to check and adjust on this bike. It depends on the build quality of each riders bike though to get the best method of aligning the rear wheel.