So I have a few more Guile questions:
1) Is there any difference between his f+MK/HK?
F+MK is faster but F+HK can start combos and is unthrowable during the later startup frames.
2) How do I win zoning wars with Guile? Characters who have QCF fireballs can spam all day and if I mess up a charge I start losing momentum. I know I am supposed to close the distance with back + LK then do L Sonic Boom at close range, punish them with forward + HP.
To win the zoning war, you often need the life lead and more meter than the opponent. It's tough for Guile to outright win the fireball war but he can definitely match fireballs. You need to create situations where the opponent is forced to take a risk such as jumping in or throwing a badly spaced fireball. If you lose momentum, just neutral jump or focus the fireball and reset the situation. Also, don't be afraid to just walk forward and block. You don't need to rely on back+lk just because it maintains your charge. You'll probably get hit by a fireball if you try using that normal to get in.
3) Should I be using Guile's close HK to counter throws?
It's throw invulnerability takes too long to start up as an answer to throws (I think it starts at the 5th or 6th frame). It's pretty good against people who crouch tech a lot on wakeup.
*General Focus Attack game play. I don't really know how to effectively use it and worse I mess up my charges trying to counter hit with FA. In training mode I can do cr.MP into Flash Kick but in a match I have only done it a couple of times.
You definitely don't want to use FA to counter hit people...it's just too slow. Only a few characters are actually safe after a level 1 focus attack dash and Guile isn't one of them. As guile, you probably only want to use FA to build your ultra meter. If you actually crumple an opponent, try doing df+hk into flash kick or f+hp. It's probably easier and more damage than cr.mp into flash kick.
*Comboing into ultra. Again this is part of the FA game. In training mode I have figured out that I have more success with back dash FA into ultra. Still not easy for me, I either mess up the dash or I mess up the charge.
You don't have to dash out of the focus animation to do your ultra. Just do it as soon as you recover.