Counter-Hitting with a F. Shoryu-FADC-Ultra will get you full animation Ultra when hit. Counter-Hitting F.Shoryu will aslo get them off the ground without the full hits of the F.Shoryu.
I also think you need to work on comboing into Ken’s ultra besides FADC’ing.
For example, you can do a cross-up Roundhouse Air Tatsu to Ultra, which gives you full animation.
AA Strong Shoryu to Ultra is another good way, but hard to time since the AA Strong Shoryu needs to be close to the corner for it to work, and also the Strong Shoryu needs to hit when they hit the tip of his fist to get the Ultra in.
Another way I personally like to combo into Ken’s Ultra is to do Super into Ultra. This only works on the corner, but deals about 650-700 damage depending on what other moves you added in before the Super. When you activate the Super in the corner, right when Ken’s feet hit the ground, activate the ultra. If done right, during the Ultra activation animation, you’ll barely see the shoulders of the opponent, this will combo in the Ultra, but not the full animation Ultra.
I like this Super to Ultra combo because it’s flashy and it deals quite a lot of damage, but I also wastes bars if the Super is blocked, and you have to reserve your EX meter for quite some time to get this.
I would try to mess around in training mode, and try to find out a good way for you to combo into Ken’s Ultra, and then fit it into your play-style during matches.
Hope this helps a little.