Legal matters: making non-open access content available publicly (mathematics/software context)
I'll answer the first question because that's what I'm familiar with. Copyright attaches to a concrete piece of text (or other ways of dissemination, such as music, but that's not relevant to us here). So, in your context, that would be (i) the paper that describes the software, and (ii) the source code of the software. But it does not apply to the idea that is behind the software, and consequently the copyright in the paper that describes the software does not also cover the software itself (unless, of course, you have put the software into supplemental matter for the paper and signed over copyright for that as well -- but you said that you didn't). 

As a consequence, even though you have published the paper about the software, you still have the copyright of the software and can do with it as you please -- including making it open source.