How is your ability to read when you should (and shouldn't) focus absorb stuff? It works really well as a counter to some things, especially on Fei as he has one of the fastest, farthest reaching FAs in the game.
Other than that, there's no getting around the fact that Fei makes himself vulnerable constantly in SF4, compared to his relatively safe pressure in HDR.
EDIT: Just put in a little Chun practice on SF4 -- Arek, there is a sweet 1-frame link worth learning on her. I got j. fp x2, s. fp --> medium fireball --> b. mk x3 EX SBK to all link in one combo for just short of 400 damage on a crouching opponent in the corner. Continuing the combo post-fireball is the 1 frame, and it's the hardest read for me yet as I usually don't have to react _right_ after I throw an MP fireball (the kind I throw the most often, as the jab version sticks her arm too far out). Credit to darklightjg1 on shoryuken for the combo. From the looks of things, if you're perfect you may be able to combo d. fp --> medium whirlwind kick --> super after the fireball also, but I don't have the time to try it myself.
Also on Chun, her best meterless combo (that I've found) after focus attack remains backdash, jump forward, d.mk x3. I'd love to be able to make something else work without meter but I haven't found anything.