So I've been watching play-throughs on Manor Lords. Like most medieval city builders, you start by building a storehouse to shelter your supplies, then you go and gather wood, and finally build some houses, a church, and the farms. It got me wondering how historically accurate this framework was.
I have a previous answer that might help with your first question at least. I wrote about how a new town was founded, or how new rights were granted to a pre-existing town, with examples from two towns in France (Saint-Aubin-du-Cormier and Lorris) and one from crusader Jerusalem (Bethgibelin).
Hopefully we will get more answers dealing with your two other questions!