1. That's your personal pref. I think it's nice that you can make better gear, that all your investment into crafting pays off.
2. I can sort of understand that one. If you are OCD about finishing checklists this will drive you crazy. I'd say ignore it, as I have when I realized that I killed/let die the NPC that 'ends' the quest, but i guess that depends on your tolerance.
3. You need to unlock the portals in the homestead, not just obtain the inert stones. Talk to zixzax to get the others open. If that doesn't help, maybe you are missing a quest (hint: the large flaming temple NW on Luculla map)
