You need to keep them as high in the air as you can while keeping them low enough to hit with both jabs before the jump kick. It is near impossible to do on Shang and Liu as they have difficult hitboxes. On the male ninjas, I'd recommend aaHP,LP instead of two high punches, they are wierd to hit sometimes in juggles. Make sure you are cancelling the second jab with run so you recover faster and can jump kick them sooner, which keeps them higher in the air.
If you are near a corner and you freeze them in the air, run them a little closer to the corner then do the aaHP, freeze. From here you can do the aaHP,HP, JK, HK combo which does 50% and relatively easy to setup given the time you have for placement between freezes. If they are high enough in the air and you are in the right place, you can get an aaHP,HP, JK, RH, HK. usub ftw!