No, my wife's phone is not rooted as of now.
You'll need two apps to diagnose. First is
CPU Spy. The other is
GSam Battery Monitor (previously Badass battery). Install both and then open CPU Spy and make sure it's recording your cpu states. Now just use your phone like normal for a bit and let those two apps run in the background collecting data.
After a bit open up CPU Spy and see if your phone is going into deep sleep. You may have to hit the menu key, then refresh to get the current reading. Deep sleep should be the bottom slot. As long as you're going into deep sleep you should be good to go.
If you have 0% deep sleep, you'll know you have issues with an app wakelock keeping your phone awake constantly. I'll make a quick note here: most phones can't enter deep sleep while charging, to my surprise, my wife's GS3 does. However, to be certain, I'd run this test with the phone UNPLUGGED from the charger.
Moving on. If you've determined you're not deep sleeping, open up GSam and look at what's using your battery. Screen should be one of your highest offenders. Radio should add a bit as well. The highest will probably be app usage. Click on app usage and it will bring up a detailed view. Are those the normal apps you use? Don't anything seem abnormally high?
The bug your mention about the corrupt sd card will show under System (*wakelock*) and the process will be called mediaserver. Click on system to see this. If system is in the 1-5% range you're probably fine.
The wakelock that I DID diagnose on her phone was caused by Google+ instant upload. For some reason it wasn't uploading pictures properly and was keeping the device awake the entire time. I had to manually force the picture uploads under the Google+ settings and all was good after that. Now it sleeps like a baby and pictures upload the way they should.