I've only played the Yor a couple of times but in terms of 'getting planets up and running' after under colonizing (for good reason since you're trying to grab grab grab with your strategy) I tended to have one production planet manufacturing yor on a steady stream and picking those up with a troop transport and moving it to colonies that had lower pops and production themselves. Manufacturing Yor on a research world is suboptimal I think compared to shipping it from a world that can turn them out en masse.

Re: factory spam - population mid-game yields huge amounts of production so I would avoid ever letting a planet hit pop cap, keep adding more until a core factory and related bonus buildings ring is all that's not pop/happiness related. That seems to yield way more production than a small pop with every tile taken up with factories and bonus yielding buildings.

The key to the economic side of the game is understanding the importance of population, morale and their subsequent effects on raw production in the midgame. A few tips:

1) the planetary governance (raw production +10/20/30/40/50) tech line is utterly amazing. Grab techs from it when they are available as soon as they are available.

2) the pop growth tech line is also really important. 

3) don't underestimate morale. It's important. Raw production and pop growth are crucial stats to achieve a strong midgame economy. Morale gives you both of those. 

4) try hard to ensure your planets don't run into the pop cap. Look at how fast they are growing - if they get within a few turns of hitting pop cap then demolish a building and replace it with a farm. The farming tech line really helps in this regard. Otherwise build a colony ship and either colonise a new planet or send it to a low pop existing one.

5) don't overprioritise the factory or lab lines. rushing down these tech trees may seem like the secret to a good economy, but your buildings take a while to upgrade and if our planets are not close to done upgrading to your current tier there is little point progressing further down the tree.

6) techs like these "gives a bonus 10% research" are nowhere near as good as they sound. The net effect to your empire is not +10% research. In most cases it's +1-3%. This is due to the way these techs stack with facoriess and labs. On the other hand, techs that give raw production, food or growth % increases are really good. 

All very good information. I will admit I have spent far more time going after factory and lab techs than I would like to admit. It is exactly these kinds of under the hood mechanics that give me fits. I havent found any good explinations for these things anywhere (yet). It would be nice to see some of these mechanics spread out on a wiki or something.

I am definitely going to put your advice into action.