Okay, that didn't work out quite the way I'd planned....
For infected it says that this occurs at step 4 of character creation. This is after Magic is chosen, so does that mean that if I took Priority A for magic, and then took the Vampire quality - my magic and essence would go down to 1 each at the beginning of play? Or do I keep the 6 in each assuming that they have fed at some point before play starts.
When you're building a Strain I Infected character from scratch, you start with (starting Essence) - 1 and (starting Magic) - 1, with a minimum Magic of 1; you're assumed to have been Infected for a little while, though you're still a basic newbie and a little hungry. You can get that Magic point back using the rules on page 141; it's not really lost, just blocked off.
If your character isn't Awakened, your Magic is set at 1. I didn't make this as clear as I should have on page 141, and I'm sorry (though it is mentioned in the disease description for HMHVV Strain I on page 142; I should have at least pointed you there on page 141).
Strain II and III Infected start with their Essence and Magic at one less than when they started, per the rules on page 141. If they don't start out Awakened, then their Magic is also set at 1.
Seems to be a hefty tax there if not- might actually make aspected infected viable... actually, can you play an aspected Vampire?
Absolutely, if you choose to do so and that's where you put your Magic priority. I'd love to see some examples of aspected Infected if people wanna put up some of those builds. They sound like they could be fun.
That brings up my other main hurdle - the qualities that indicate that the subject awakens. Most give a discount for already being awakened; but for those that are not - what type of awakened would they be? Full magician, but with no spells and skills from the priority chart?
Only three of the Infected types automatically Awaken as some form of magician: mutaqua, nosferatu, and wendigos. That's why they offer a Karma discount if you're already magically active. I might have phrased that better; sorry.
None of the others automatically make you some sort of magic user, though there is a possibility of that. The chargen rules assume you were either Awakened going in, or the virus Awakened you as part of your back story. If you contract the virus during play, you might Awaken as a magic user at the GM's discretion, but I didn't have room to include specific rules for this. Kevin and I are pitching a "Way of the Infected" type e-book which would have a lot of the more advanced stuff...like Awakening as a result of Infection.
This is the part where i wish they included an example of character creation for an infected.
I wish we'd had space to do one, but Kevin and I were both up against it in terms of word-count. In retrospect, I wish we'd asked for a little more space, but then something else would have had to be cut.
That said, I'll try to put one together and post it here in the near future.
Would a Soykaf addict who gets Infected and becomes a vamp prefer to prey on Heavy Soykaf users to get both his blood and caffeine fix seeing as he can't drink straight soykaf any longer? 
Well, that's how
I'd do it, but your mileage may vary. I think I mentioned in fiction somewhere about an alcoholic vampire who prays on drunks, but I might have just imagined that.
I take your silence for "Formulating a satisfactory answer takes way longer than I anticipated". 
The day became a touch more interesting than I would have liked.
I don't think you can thin Soykaf with blood to make it Vampire-Compatible.
You could enrich a specimen with a lot of Soykaf before your meal, however.
Maybe you could inject raw caffeine into a bloodpack? Same deal. Patches could work.
You're right about the mixing. I'm not positive about patches....
