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.   

Need to chek chain tension all the time. Also the manual says to lube the chain every 500mile. It's important part of service of any type of bike. Did you use a torque wrench to retighten the axle nut? You should or you might overtighten and damage hub. You need to use a torque wrench.

Also when retightening the rear axle you must check wheel alignment as adjustment of the chain tensioners will probably cause wheel alignment to become incorrect. This could cause chain links to be stressed and sprockets could suffer premature wear. Best to get a bike shop to reacheck your adjustment.