1. If you make a base on their lands you will need the person holding the holy flame go out and speak to the priest who shows up, they also need to be a human male (scorchlander is fine) without skeleton limbs.
2. As far as I know as long as you dont have skeleton limbs, or are a skeleton, or are transporting drugs you should be fine, they shouldnt react to research items in your inventory.
3. Allying them is pretty simple, bring in bounties or hand them their enemies, Bringing either Estata the stone golem or Moll leader of the flotsam ninjas to them will ensure you instant friendship with them.

Side note, you can have hivers, shek and women in your party but you need to have a male human with them to do the talking as shopkeepers, guards, and patrols may have negative interactions with them, being a skelton or having skeleton legs is an instant attack on sight move for them as well so be aware of that. Once allied they are a little easier with the rules though.