The issue with having progression based on days is that you have my issue where I would rather wait for all the resources to be discovered before even setting up any trade routes. This means that there is at least a minute of downtime before a player really wants to start the game.
As for resource discovery being dependent on population, the logic is that as your main market grows, the civilization grows along with it. More population = more advanced eras. You don't just wait for time to pass before you get to the iron age. You have the population grow and advance. It's not just time that causes advancement. It's people and time.
As for the other possibilities, they don't fix the core issue of not feeling like playing the game until all resources are shown. Because what's the point? A bad solution would have money decrease over time so that the player can't sit on their ass for the first 1500 turns, but that's just annoying imo.
You already have a good system for determining whether a player understands how the resources work through the population demand window. So once they get the resources demanded, then the next resource appears. This would be good design and would ease the players into learning about each resource.
That's another issue with having advancement based on time. The player doesn't get enough time to fiddle around with each resource before another one is suddenly thrust onto the field.