Disclaimer: I am not an expert, feel free to question this advice.
I’ve found that a very useful thing to remember against Guile is that he cannot use his flash kick for a short time after throwing a sonic boom, so you’ve got a short window of time where it’s relatively safe to jump over that boom or buttslam him. On the other hand, be extremely careful if he doesn’t throw a boom for a short while as that probably means he’s preparing for a flash kick.
The towards+roundhouse far sweep is also pretty useful to punish his pokes as it outranges his normals and can trade with booms in your advantage.
Bulldogging is often very difficult against him because of his incredible recovery after booms, a good Guile will throw you enough booms to push you back from blocking the booms so you won’t actually advance anywhere. Some Hondas like jumping straight up with the controllable FP but once again that doesn’t let you go anywhere and mistiming the jumps is dangerous. Against a good Guile, your only real option from a far distance is to just jump over booms or SK/MK buttslam through them instead. HK buttslam is pretty dangerous to use to advance, though, since it’s fairly easy to counter. I try to only use the HK buttslam if I’m sure it’ll actually hit Guile, and never use it just to advance. In any case, where you want to get is just out of range of his sweeps, from there you can punish whatever he does.
But Honda vs Turtle Guile still remains a lot of guesswork and mind games for me. I often do buttslam+HHS or far sweep if I guess he’s going to boom. Far sweeps are also useful against pokes, and sometimes Guile gets twitchy enough with them that he’ll try to psychic Flash Kick them, which often fails and nets you a free hit. If he gets afraid to throw booms (i.e. he’s storing his Flash Kick and waiting for you to jump) I’ll just MP HHS him for tick damage, since it’s impossible for him to Flash Kick you on reaction. If you’re at the right distance, even if he does throw a boom the MP HHS will often trade anyway, and most pokes will be cleanly stuffed. Learn to recognize that distance and be ready to HHS him for free tick (or counter!) damage.
Technically you could also try a walk-up grab, but most Guiles will poke too much for that to be viable and you’ll usually be a bit too far for it to be much of a surprise.
But all these depend on your ability to predict your opponent. The scariest Guiles are those who can reversal Flash Kick only after they see you start a move to tick-damage them, like a buttslam+HHS. Perhaps the safest thing to do after you score a knockdown is to get close to him and try a negative-edge Oochio - if he tries a reversal Flash Kick you’ll just block him, if he tries to block or poke you’ll get the throw. It’s often hard to get into range fast enough, and it’s still pretty dangerous if he decides to go for the counter-throw, but you can train him to not do that by doing meaty far sweeps instead, once in a while.
A crazy thing I like to do in combination with that is to use a buttslam to get close to him as he gets up, but purposefully do it early so I either land before he gets up, or it counts as a safe jump and I’m safe from reversal Flash Kicks anyway. And then do the negative edge Oochio stuff. Bonus points if it crosses up! You have to do it really early though. Often Guile will try to reversal Flash Kick it since the move is so obvious, but since you’re already landed and blocking you’ll get the advantage. Then maybe mix it up by sometimes actually hitting him with the buttslam+HHS for some sweet tick damage so he never knows whether to reversal flash kick or not - that’s much more dangerous to do against reversal fiends but it does increase your psychological “fear factor”.
Overall, though, the only “safe” thing you can do is use that small safe window after a boom to jump-in FP or buttslam and do some tick damage - and that depends a lot on your reflexes… Generally I try more to win the psychological war against Guile because he can technically psychic Flash Kick me anytime else than after a missed boom if he’s calm enough, so I want to do everything I can to upset him and make him lose his concentration. Where Guile thrives on regularness and predictability, you prefer chaos to happen and screw his well-timed patterns. So don’t be afraid to take gambles and try to guess his moves because overall you’ll generally get more out of correct guesses than Guile will out of your mispredictions. Honda vs Turtle Guile must really get into Guile’s mind to win the match, both to predict his actions and to instill paralysing fear.