Use the software from the official PA Soft developer's website. Does nobody bother to check that its available for free?
There is no pirated version. It doesn't need to be pirated if it's free. Go ahead try it out, there is NO difference between the two.
Good luck on finding a manual. There isn't one. Just lurk bimmerforums coding section, there are a couple of write ups on the software. It is pretty straightforward to understand. An OP, those first sets of shadow codes you provided are engineering codes, they don't apply to your car, disregard.