getting an ota to work requireds the following:
-be on the current "release" version(not a leak)
-be running the stock recovery
-be pretty much stock. modifying the rom,deleting bloatware,etc. will cause the update to fail.
since you are downloaidng the OTA,the 2nd and/or 3rd requirements are prolly not being met.
IF you are running the stock recovery,and have a backup of your stock rom,with all the bloat,etc,in place you can restore it and the OTA will work.
if youre running a custom recovery,you can try restoring a stock,unmodded backup,then reinstalling the stock recovery.
the best thing for you to do,IMO, is to simply relock and run the ruu for the newest update.
download from here: Shipped ROMs
-install update in hboot(place on sd card,rename PH98IMG,boot to hboot)
-reinstall,or launch recovery
-make a stock unrooted backup
-install superuser in recovery.
you can find superuser here: http://forum.xda-developers.com/showthread.php?t=1538053
(download link that says "CWM-SuperSU-v0.96.zip")
more info starting here: Scottys noob friendly root guide-start to finish