I don't know the answer to your last question Pharaoh (what an appropriate name), but something that helped me a lot in understanding basic item crafting / modifying is that: every item of the same type, at its max, is the same. I'll try to explain what I mean in the easiest possible way since it might sound confusing if I don't proceed with care
Say your wizard has just started and you see that he has a level 1 wand equipped already. It's important to know that that wand has the capability to be upgraded (using the appropriate crystals) and to be maxed out to be identical to the "best" wand in the game, with two exceptions - there are a few Ruby affixes and Set Affixes which can only be found already on an item and cannot be added to one using crystals.
I want to make this even easier for you since it's still confusing I think. Let's both do this: in the game click on the Codex, then LegendEx, Then click Wizard. These are, if you don't already know, all of the fixed Legendary items you can loot in the game. Unless you find one that's an Eternal Rare, they are otherwise all modify-able.
Right then, so on the 1st page we see an item called 'Livid's Wicked Wand'. It's not especially rare, especially unrare, nor especially anything else (CS Lewis). Now let's move ahead 14 pages in the Wizard LegendEx section. We see another wand here called 'Aether Spark', which is slightly harder to obtain because you don't find it until floor 400+. But here is the key - these two wands, if you removed all of their affixes (using Larimar or Quartz crystals), would both boil down to be the exact same Basic Wand. Provided that they are the same Quality and Level (also modify-able with crystals), they will have the exact same damage and abilities). So now that you know that, you know that any item, with enough crystals, can be modified to be the most "powerful" item, whatever you think that may be. I believe this is the foundation of item crafting in the game.
Here's the catch though, and something you only learn as you keep playing. If we look again at Aether Spark in the LegendEx we see:
Aethereal Drain = set bonus
Multi Attack, Glasscannon and Push the Limit = Ruby affixes
Arcane Dmg + = Epic affix
Empty Socket = Rare affix
If we put what I just said into practice and spend a ton of crystals on our level 1 wand, we would see / discover we could make it identical to Aether Spark, with one exception - and this exception alone may be what makes this wand more valuable to us - Aether Spark as it is looted has the Ruby affix called 'Push the Limit'. This affix cannot be rolled onto an item using a Ruby, it can only be found already inside of an item. So with this in mind, the one and only thing that makes this wand any better than my level 1 wand which I plan to modify a ton, is this affix alone. I could be scowering floors looking for Aether Spark JUST so I can remove all the affixes except Push the Limit and craft something else entirely with that as the initial molding so to speak. (Note that the Wiki link I'm about to paste below says that Push the Limit, in particular, is a roll-able affix using Ruby. It is not. I think that's one of the only mistakes on the page though.) it's actually more complicated than this once you consider that items can be switched to other classes so you might actually want Aether Spark for its Push the Limit affix with the actual intent of using a Jasper on it to turn it into a weapon for your Warrior that you want to modify and build on.
So you see, the key then is to learn which Ruby (and Amethyst / green) affixes can be rolled and which can only be found already attached to an item. This factor alone necessitates you having a particular looted item to perfect your build down the road when you get to that point.
All affixes, along with whether or not you can roll them, are listed here: http://dungeonquest.wikia.com/wiki/Affixes
I'll have to re read this and edit some things perhaps, but I hope that makes sense.
Also a few Set affixes which are unrollable with Amethyst include Epiphany, Nadroji, Cerebral Vortex, Crystallized, Eternallized, among others.
Here's another tip that will really help you I think as your farming:
^^ i.e. These items have unique Ruby and/or Set affixes which cannot be rolled with crystals, only looted