Rooting with CF auto root or framaroot wont touch any app or widgets.
Rooting by flashing a pre-rooted custom or kernel might effect some of the apps

how you root your device and you in custom or stock? flashed custom kernel..

try reset cache first..

read below and follow step in Wipe cache partition, don't do master reset where it will wipe your phone totally and all your data will gone..

http://support.t-mobile.com/docs/DOC-6205

Bro... can't recall what is your problem already... mind to repeat it?

1. May i know what do you mean by Widgets not refreshing on home screen.
widgets like clock doesnt reflect to the correct/current time.

2. For whatapps notification what do you mean whatapps notification not showing? If you referring to when message came in and whatapps not notifying you, please check below.

    - is your "Show notifications" is ticked? Go to Settings -> Applications Manager -> Under download scroll to Whatapps, please tick "show notification

    - If you have tick "Show Notification" please check you whatapss, do you set your notification popup and light..

Referring to no notification when msg arrive (i dont even know got msg until i manually open Whatsapp).
Show notification is ticked, and no-popup but enabled light (by right it would vibrate & show icon on notification eventhough no-popup selected but now NOTHING).

Just wondering you disable anything from settings -> Applications manager -> ALL?

Bloatware cannot be simply disabled or removed.  Now only thing you can do is use odin to flash rom again. .

flash the zip file in recovery
then choose what software you want when in a special installer (its call aroma installer)

You sound very new in flashing. Do all reading before doing so. First thing to do is solved your problem you mentioned here otherwise you will be in dead end..

Glad to know this is not hard. What root method you use?

You may have changed something...

You in stock, right? my suggestion is you use odin to flash the rom back to stock first, before doing it do a backup first  even if the flashing will not master reset your phone then only you root it again. After that check if your phone still with the weird things you mentioned...