1. There's currently no population limit. This is not decided upon yet.
2. The Clay Pit takes a lot of digging, so the ground becomes unsuitable for placing buildings or farming. Only 1 or 2 of the planned factions will require clay for constructing buildings though. Also, you will be able to place Clay Pit next to a river when we add that to the game.
3. This sounds like a bug we need to investigate. Thanks for letting us know!
Thanks for your encouraging words!