I'm kinda a noob to all this, but from what I read when I rooted everyone said to not delete any factory apps, just freeze them. The missing apps may be what is blocking your update. I'm not sure how to get them back, you can probably search around for a fresh stock install or something. I'm trying to figure it out for my phone today, will update if I find anything useful.
Do u know were or how to find the factory software? And if you find anything usefully please let me know. I know that new update fixes all the bugs in our phones. And if I got back to factory and reroot I should just freeze apps not remove them