I main Sakura, I know she is in in lower tier of fighters but I'm too deep into the learning process to back out now. As you know she is a Shoto which makes her easy to pick up and play, her biggest advantage on the battlefield is that she can punish almost anything with her crouching fierce punch(shorthand for that?) and her crouching medium kick. Almost anything, I have been having no luck against  other Shotos such as Ken and Akuma. I can punish their hurricane kicks with a crouching fierce punch, but I can't find a punich against close range fireballs and Ken's SRK. Any help would be appreciated. 

If Ken's srk is too fast for you to punish with crouching fierce why dont you use crouching jab, it links into crouching fierce. For close range fireballs you could use her focus attack which travels pretty far so you can absorb the hit and get a crumple.

It's actually easier if you bait the srk than punishing it ahead of time.  After he throws the shoryuken, link the crouching jab, then crouching fierce punch then EX tatsu with the jump smash thingy. 
 
Actually, utilize sakura's focus attack since it has a really good range, then punish.  Most of the sakuras I've played online really make use of her focus attack and her tatsu, varied from short to EX.

Sure, works....against bad players

dont  jump at a shoto you will eat a shoryuken