Hmm…from what I’ve experienced…notes…
EX CW over lp Sonic Boom = counterhit :lp: or st. Fierce Punch/crossover or whiff (Yeah, it does knock out an EX CW when it enters it’s projectile invulnerability state).
Jumping over sonic booms = a big no no. Unless you’re really close up and going for a crossup which is bonus points.
cr.lp > overhead usually thwarts them off their downback charge as they’re usually accustomed to blocking two hit chains before reversal Flashkicking the third hit. At times, depending on range, the overhead also cleared over sonic booms as well. Bonus points.
Flashkick, I can usually stuff with an early or well placed j.mp > Tenshin/grab/cr.lp > overhead/blockstring
Crossup attempts on Guile nowadays are more thwarted by a FADC forward or forward dash. But usually ends with them in a defensive state anyways as they’ve lost charge completely so I can continue pressuring regardless.
Guile’s low forward follow up from sonic boom, I usually counter by blocking the sb and throwing a lk/mk CW reversal land on Guile or cross him up. Or I’ll throw a quick overhead to hop over his low forward and counterhit.
One thing I forgot to mention about Guile’s lp sonic boom follow ups is where he’s standing (behind the boom, inside the boom or way behind the boom).
We all know the tricks to Guile’s cr.hk so I’m not even going to bother mentioning that. lol
Yeah, I guess you’re right, Nosone. 
Edit: A hint of a good guile player is when they’re charge buffering off of normal attacks (whiffing back + mk, whiffing back + lk or random excessive jabbing). These are the types that move across the stage not by walking but using their normals to cover ground while buffering their charges at the same time so they’re almost always locked and loaded.
Most of my friends whom use Guile are aggressive types. They seem spastic but they’ve got great zoning and control throughout the stage.