Good to know about soul gems, I never got one yet. One thing I noticed is that when killing random invaders (and I think even animals) with my sect leader, he got "Condemnation" from it (bad karma basically). I think it's because they were of a lower stage than him.
As for sect feng shui, I can definitely confirm that it gives a bonus (or malus) during breakthroughs, you can see it in the breakthrough window.
For wells, I can confirm that wooden wells get a bonus, because the building naturally generates water element, which feeds the wood and makes it auspiciuous.
Similarly, a stove, forge or furnace emits fire, so you get a bonus when making them from earth materials (stone basically).
Also, how to I unlock the simple, ordinary furnace? I think I've built everything, yet it remains hidden.
EDIT: Nevermind, just need to wait I guess. Or maybe build a building, I dunno.
About that, I think that you unlock pretty much everything as soon as you establish your sect, which can be right at the beginning of the game if you just give the free foundation pill to whoever you want as sect leader and make him breakthrough on the spot. The annoying part is that only outer disciples can do regular work, so you have to plan around that.
Another useful tip : you don't have to mark and haul everything you want to trade, to the trade area. Instead you can just check "available for sale" in any storage area, and everything in there will appear during trades.