Re: Process mapping prior to validation, and software to use to map
Before going too far down a rabbit-hole, take a step back and recognize that the only thing you NEED to do is to validate those processes whose outputs are not / cannot be verified (and software used in the implementation of the processes or the quality system).
Certainly, mapping is a handy tool.
I've always found it's best to figure out how you do things and then find tools that align. You might try something as simple as Visio (or similar basic drawing / mapping tools) just to get the processes down on 'paper' for discussion. And instead of going first for tools, consider the methods that work best for you (flowcharts, swimlanes, etc.)