Actually, I think there's a precedent if you use an opposed test vs. Object Resistance. i.e. seawater would be different from a mountain then -- and a mountain different from a concrete wall versus a pile of dirt. This would affect the number of net hits you get, thus affect perhaps the "amount of material removed" from the object. Or perhaps the net hits affects the rating of the weapon created from the material. Obviously if there's no net hits, the spell is ineffective. The basic point is, such as in native american philosophy -- EVERYTHING is "alive" or imbued with essence/spirit, and thus even non-living objects can resist your magic.
There's also, I believe, some historical precedent for at least the separate material spell. The only game-balance issue I can tell is that it takes a judgement call on how much of X material is even available in Y object. Actually, there's one more issue: Line of sight. Pulling iron from a mountain -- unless you're right near an iron ore deposit, you would never affect the entire mountain, so what amount of iron would you pull from the mountain? You need a creative & resourceful GM who would be able to make this call on-the-fly... how much mountain is "one object"? How much seawater? You certainly could not desalinate the whole ocean. However, desalinating a bucket of water -- perhaps. I don't think that's imbalanced. Perhaps even a swimming pool worth of seawater...
How much of this is teleport or telekinesis would have to be decided. If you separate water from seawater -- what's the receiving receptacle? How does it get from Point A to Point B? Do you need 2 buckets?
So I'd say this would need more thought on the mechanics -- it would have to "make magical sense". Exactly how is it doing it? It can defy scientific explanation, but must follow the "rules" of manipulation spells.
As for pulling iron from a mountain with one spell, then creating a sword with it -- as 2 separate spells -- I'd make net hits also represent the quality of said weapon. At 1 net hit, you have basically an iron bar. At 2, a crude sword. Nothing to write home about. At 3, you'd have a passable sword. At 4, a good sword. etc. From there, perhaps use the Shadowrun stats for normal swords with perhaps a modifier on the amount of damage it does (-2 for 1 net hits, -1 for 2 net hits, 0 at 3 ... with a max of +1 over the damage of a normal ShadowRun sword?).
Would this be a sustained spell effect or permanent magic? That would be one of the big factors in drain. Frankly, I'd be more inclined to allow this "make crude weapon from stuff" spell if it were sustained. If you learn anything about real swords (Inconnu: I know you watched at least one sword documentary, so you can't dodge this...), they are much more complicated than simply fusing together a bunch of iron molecules. If you melt iron and pour it into a mold in the shape of a sword -- that is one of the world's weakest/most brittle and crudest weapons ever -- not to mention susceptible to rust and unlikely to hold an edge....