Here's the filesystem layout for the Evo 4G LTE, a little different from your 3D but still, HTC's basic overall Android layout. (click to enlarge)
In this case, the system partition and the /system folder mean the same thing. Ignore any dates you see in there. Ignore zero sized files.
Ignore everything under /dev.
In fact, all you really might care about as far as deciding if things are corrupted would be under /data or /sdcard folders.
If timestamped dates have been corrupted, they've been corrupted. You're not going to fix them without backing up, reformatting, and restoring for the SD card and not at all for /data unless you're rooted, and then by going the same route.
Unless something time-sensitive is broken, I wouldn't sweat the timestamps a whole lot but that's just me.
Btw - your phone may never glitch again or it may too. Glitches cannot be prevented.
Not everything with a null timestamp was glitched.
I'm starting to get lost, to be honest.
Please tell me again what's broken when you use your phone, thanks.
