I'm not sure if the element of your tool matters at all tbh, as far as i noticed its too negligible to notice/care about. Artifact element definitely matters though, you should pick a element for your artifact that is fed by the element that your cultivators law is.
If you improve the feng-shui of your well by making sure the area around it the element that feeds it (or if its in a room, also the quality of the room), i think it performs better. I'm not sure you'll notice the difference on specifically a well... maybe if you have like really bad feng shui people will get injured on your well sometimes, pretty sure feng shui effects accident chances quite a bit, it should also increase/decrease chance of better quality stuff in most workshops, but i think water is one of the base-materials and thus, has the same quality regardless. Oh, and peoples opinion go up when they are near attractive things and high feng shui things (and down from the inverse).
Uhh to be clear if your well was built in a area of high-earth, you should build it metal which feeds on it. once you get the observatory you can see specifically the fengshui of a object or location (which isn't JUST element, some stuff like what side of the room doors on matters a lot... or how crowded/empty a room is, or how nice the stuff in the room is)
Yeah spirit stones, useful, never have enough. For the record, in addition to buying/selling to the merchant that comes a few times a year, you can also trade directly with sects on the map once you 'talk' to them once, (which is just giving them a gift on the map scree, if you give them a shitty gift you don't get negative opinion or anything so dont worry). Finally if you buy a auction permit ONCE, you can visit the auction house that happens fairly often, as many times as you want. Tons of ways to use spirit stones.
Oh, and spirit stones are used in a lot of recipes, lots of structures use them, alchemy uses them for some stuff, like spirit crystals.