Mr. Miyagi gives the best advice for this.
Anti air with HP Shoryuken as it has 6 frames of invincibility which is more than any other characters Shoryuken except Seths. It’s difficult to describe how to time it; but my best timing for it is to do it so that the command is finished and the Shoryu starts as they are at my head height. I can’t say what point of their jump that I actually start the command. This is what works best for me since I don’t like trying to do super-late Shoryu’s either. It doesn’t always get 3 hits but it wins a lot.
The crouch technique basicly helps you with doing late ones by lowering your hurtbox until they come down to a point where the deep SRK gets the best priority and all the 3 hits. Done correctly, it has pretty much unstoppable prioirity over frontal jump-ins; although I don’t personally like trying it. You need to experiment and refine your method over time to find what’s best for you.
Remember that many of the jump attacks are different and require different timings and are more or less effective at different jump angles. Some jump attacks have hitboxes that are on a slant reaching lower, rather than a horizontal angle like Ryus, so they don’t have to wait as long to drop low enough to hit you and thus you have to make the necessary timing adjustments accordingly. The timing I described for what I use is what I personally find requires the least adjustment in the majority of situations to beat their attack; even if it’s not the optimum timing for common jumps.
Also be aware that HP Shoryu is only one tool of Akuma’s set that’s needed to control the air. It works on frontal jumps that fall directly into it’s sweet spot. You need to command at least cr.HP, HP Shoryu and far HP for a strong control of the air as these extra attacks cover angles, ranges and situations that Shoryu doesn’t. Consult the anti air thread for further information about these.
(called “Jumping into a Spiked Wall”)