Here I come!
Well, the obvious advice to give here is to improve your execution. That’s something that will just take time. You don’t want to get into a fireball war with Ryu for obvious reasons, you want to wind up in his face to remove that advantage. Either use a Focus Attack to absorb a fireball and then dash closer (ready to block the next if he immediately throws another), or jump in carefully over the fireballs. Don’t jump in predictably, or you might eat a Shoryuken. Don’t jump at all once he gets his Ultra, because you can bet he’s looking for the easy anti-air into Ultra combo.
Once you’re inside, I don’t want to say you have the advantage, but it’s a lot better matched. Control him with the Knee of Justice (LK Danku) and heavily punish any mistakes he makes. The Knee against his wakeup trades hits with the LP Shoryuken and evades the HP/EX Shoryuken, so if you’re not sure what he’ll do when he gets up, the Knee isn’t a bad bet. If you’re sure he’ll do a wakeup Shoryuken, just block and punish. Punish with c.HP > HK Danku whenever possible, or s.MP > HK Danku if you don’t have the timing down on the excessively slow c.HP yet.
Dan’s dash is his friend for closing distances with runaway Akuma. It’ll carry you under most of his air fireballs and set you up to punish him when he lands with Dankus. Because of Akuma’s frail health, you don’t have to hit him much to win. Don’t be afraid if you take a few shots of his air fireballs, as they deal pathetic damage. Be much more wary of the strong combos he can string together with his normal moves. Most runaway Akumas aren’t interested in that strongest part of Akuma’s game, though. Against the aggressive Akumas, be careful and pick your spots. The midair Knee of Justice beats all their Demon Flip shenanigans, and if they set up air fireball traps to create ground combos, surprising them by EX Koryukening through the fireballs might catch them off-guard.
EX stocks are important here. Try to EX Danku on reaction to any of his EX Dash Punches, for the armour breaking knockdown. You can throw him out of most of his dash punches, too, but that’s hard to do reliably online. Once you get a knockdown, c.MK trumps his Headbutt wakeup and allows you to keep pressure on him. Don’t jump in on him unless it’s to cross him up, as c.HP and the Headbutt make for a strong anti-air.
Your best hope on Rufus is to mercilessly rush him down before he can do the same to you. Get in on him with Knee pressure and keep him reeling with Knees and tick throws off of Knees. Once he gets an EX stock, be aware that the EX Messiah Kick might come at any time, and be a bit more conservative. Punish it on block with a Koryuken. You can get the Koryuken out before he does the second attack on the Messiah Kick, and it’s a guaranteed hit no matter which followup he chooses. You could try an Ultra on block instead, but if he goes for the overhead followup he’ll jump over the Ultra, which sucks for you.
If you want to continue pressuring him when he has EX stocks, make sure that you’re in midair at the point that he’d use the EX Messiah Kick. That way you’ll only take one hit of it, which is pretty wasteful of his EX.
Gotta be defensive here. Jabs will beat the Blanka Ball, but the slide eats them up. The slide is very punishable on block unless it was done from maximum range. You can punish a horizontal Blanka Ball on block with an Ultra if Blanka’s doing it out of the corner, and you can punish a vertical Blanka Ball with an Ultra anywhere on block. You might get some mileage out of Koryuken/throw mixups while he’s standing up from a knockdown, but those are risky. In those cases, Koryuken will beat electricity and any wakeup ball (EX Koryuken is needed to beat EX Vertical Ball), and the throw beats electricity (when well-timed) and blocking. Never try those wakeup games when he has his Ultra charged, though, as the Ultra will beat all of the above.
Punish the Cannon Spike on block with an HK Danku. It’s easy damage, and you’ve got lots of time to do it. EX Koryuken on reaction shuts down her EX Hooligan Combo, or you can even Ultra it. The Koryuken trades with the Cannon Strike, which will set up an extra HK Danku juggle in the same vein as the Ryu anti-air trade sets up his Ultra.
If he’s just using s.HK to anti-air you, do the midair Knee to beat it clean due to the messed up timing. The midair Knee usually trades with an anti-air Tiger Uppercut as well, and avoids his Ultra. The smart thing for Sagat to do in that case is to either just block, or Focus absorb the Knee, but most Sagats aren’t that smart. 
Dodge and weave between the Tiger Shots, determine how the Sagat in particular handles close-up pressure, and then get in and take advantage. If he’s enjoying his Tiger Knees, c.MK goes right under them, causing them to whiff and giving you at least a free throw.
Ken’s fierce Shoryuken does the same amount of damage as Dan’s fierce Koryuken. So really, Ken’s offense isn’t that far ahead of Dan’s. Ken’s biggest damage comes off either the EX Shoryuken, or his Hurricane Kick combos. Against flowcharts, bait out the Shoryukens and punish with c.HP > HK Danku. If he loves the amazing bread and butter j.HK > sweep, anti-air him with a Koryuken, or just block the whole thing and wait for another opening. Once you knock Ken down, start bunnyhopping over him with the Knee. Only Ken’s medium Shoryuken will beat it on wakeup, and few Kens will think to actually use that in that situation. The Knee will eat up his other Shoryukens and should give you an easy win unless he adapts, and if he does adapt, well, you’ll need to adapt to him in turn.
Those are the guys you say you have problems with, so hopefully that helps a bit.
I’m practicing hard to become a Saikyo Master.