One method would be to watch the throw whiff animation carefully, and use it as a visual cue. Once you know 'where' the throw whiff is done, and you can perform an action again, that's the timing point for the 2nd Forward (and hold it) in the dash input. Work backwards starting your 1st forward a little before the throw whiff animation finished. If you need a little more timing work, push someone like Tager deep in the corner, and do 6A 6C (B+C) 6C (B+C) wash rinse. Once you can get 6 or more reps of the 6C consistent like, probably a good time to start working with the dash part.
Your assessment is correct about it being second nature to many of us, and that comes with lots of practice, naturally. Learning combos take a minute for basically everyone. 16 years into fighters, and I still spend some solid time in Training Mode. Keep at it, no worries pimp.