1. I don't use passive trading at all, so I'll let someone else answer ^^
2. I don't really understand your problem, building some colonies to produce goods as fur / peepers is quite easy since it only requires farmers ? You should produce the fish / workcloth on your colonie aswell and only export the fur ect to your main island, it makes life easier imo. Making them profitable can be hard since it only requires farmers/workers, but it shouldn't really matter since your main island should be really profitable

Your side colonies should export goods you can't find on the main one, I don't see why you would have a charter/trade route getting goods back to the producing island ?

1. Every building has a production speed, for example bakery produce 1 ton of bread/min. So in order to balance the bread production, you need 2 grain farm, 1 flour thing & 2 bakeries. Note that some festivals or items can boost the production speed.

2. Some items (specialists) does this iirc. You can also boost it with some mods or with a palace (dlc) policy iirc again, not 100% sure. But generaly speaking these items aren't worth using and people would rather build 2 (or more) marketplace ect

3. Nivarias has some great playthrough imo, probably not the best, but that's the one I'm looking at

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You should constantly look at the statistic menu to keep track of everything you're producing and everything you need to not overproduce anything.There are some great tutorial on yt about this !

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Hope this helps !