I think everyone is frustrated when dealing with E.Honda. Here's how I do it in the low levels.
We know, when played the time correctly, Ryu's fireball can beat his headbutt in neutral. As shown here in 0:50
Once the opponent decides to stop doing that. He'll go for the butt stomp. That's when you should anticipate his stomp, just like how you anticipate a jump over by anti-air. But in this case, use neutral jump or f.jump with him! 0:54
Another one here at 1:00
Finally, at 2:45, he decides to approached me with Drive Impact! Of course that's when the game becomes fair.