1. Needed to research that. I would rule that it doesn't count as a domain for other feats and also doesn't count as cleric spellcasting as a requirement for prestige classes (because in what I found the spellcasting in that case is VERY limited) when you cast something (and use a domain ability) it should be cleric level=character level. No changing these domains for domain feats either.
2. I'm not sure what Prestige class you may want to enter but you can consider them waived. Give a small nod in you're backstory to sate my curiosity (you don't need to be a member of the organization but I would like to know how you got the knowledge to get into that Prestige Class somehow).
3. I always forgot these, you can choose to take 2 bonus feats, no further traits or flaws. (I updated the 16 accordingly.)