7. Finding magic sites of the type of magic you want is impossible, especially when all your mages only have one level in that type of magic. Seriously how do I do it. I guess I alchemize gems then empower them?
Use site-searching spells: Augury, Auspex, Haruspex, Astral Probing, Dark Knowledge, Blood Bowl, Voice of Tiamat/Apsu, Gnome Lore. Each finds all sites of the relevant kind in a province. Each requires at most 2 levels of relevant magic path. You should be able to get at least one mage to lvl2, either by empowerment, item forging(magic boosters), random event(of the "a mage joins" kind), or by designing your pretender accordingly.
All these spells are easy to access, as they're not that far on the research ladder.
There's also an astral spell called Acashic Knowledge(not Acashic Record, mind you), that is harder to research and cast, is rather costly in pearls, but reveals ALL sites in a province it's cast on.
Additionally, there's an artifact called Book of Creation, that can cast its own, costless version of Acashic Knowledge.
Finally, one of viable strategies for pretender design, is the so-called "rainbow mage". You pick an awake chassis with very cheap cost for taking new magic paths, and increase magic to 3-4 in as many paths as you can afford. Then it's just a matter of sending him/her/it to search for magic sites, giving you a lot of gem income way before anybody else. Also great for research, forging and magical diversification later on.
6. Getting mages ranked up is critical, so leave some in your army stack so you can get guys with more then one point in magic (Research can evidently rank them up to level 1, though?)
What do you mean by that? The only "ranking up" I can think of is experience, which increases by 1 for ALL units every turn, more if they take part in battle, even more for each swing they take in actual combat.
I don't see why you think it's so important, as it merely gives your mages +1 research capability per level(along with other, less important stat boosts), which isn't that much for most mages. Certainly not enough to justify the time spent with an army and away from actual researching.