I can't say that this is your problem, but I see a lot of log messages where harvesters are returning home because the player does not own the planet to be harvested. I think you start out owning the planets in your own system, but if you go to another sector you must drop either a Mining Outpost or a Colony ship in order to harvest the planet.

If you set a harvester route, and it goes out to the source, comes back to the destination and stops, that's a pretty good indication that you don't have mining privileges at the source planet.