I practiced this on the nFBA emulator.
As you propably already know, you can link Ken's ST MP to the shippu super art. You may input qcf, qcf, any kick fast enough during the MP animation to activate sa3.
I found a new method which is slower, but it works well (It does in my case, anyway).
Tap D, F, but do not do a qcf motion, because the hadoken will come out. Now, press st MP(connects), immeadiately qcf, LK/MK/HK. You can piano all kicks for better hit confirm.
So its, D, F, ST MP(connects), D,DF,F+ LK/MK/HK or piano all kicks.
Try it. It may work for you, as well.
EDIT: ST MP is the full range/extended MP( far ST MP)