This is exactly the bug that caused me to seek out this forum.
I had the idea of setting every colony to Import AND Export the required goods (lumber, ore/tools) and keep 50 or 100. This would, over a bit of time, even out the distribution of resources among the colonies. The problem is that the wagons fill up with these resources and are left with nothing else to do.
It would take some heavy programming to fix this into something very usable and user-friendly. My suggestion is to set up both a Min and Max level of storage desired. But instead of the Min being how many units are left in storage when a wagon passes through, the Min would be the trigger that adds the colony's trade route to the trade matrix. In other words, if I set Jamestown's Min Lumber to 150, this colony's Export Trade Route wouldn't even appear in the trades routes matrix until Lumber in Jamestown is 151+. Additionally, the Max, when hit, would remove the colony's Import Trade Routes from the trade matrix.
And lastly, if a wagon comes through with cargo, it ONLY unloads enough good to max-out the warehouse. The remaining good stay on the wagon and move on to another trade route.
It would also be nice to prioritize trades routes. Nothing is more frustrating in this bug to have one colony with 300 lumber and two colonies with no lumber while the wagons are off delivering ore to a colony on the outskirts of the country.