Default Problems after Repair (Battery or Processor)

I sent my phone in for the purple camera problems and I got it back last week.
When I received it, it was updated to 4.3 Sense 5, most likely from the latest RUU.

Since I got my phone back, my battery has been horrendous and I noticed it had heat problems. I checked battery health and it said it's good, so I figured I just needed to re-calibrate my battery so I gave it a week of use. It's been the same horrible battery life.

I checked for wakelocks but there were no significant ones I haven't seen before. I've attached some screenshots of battery use. One thing that confuses me is that it shows Wifi running for 9 hours, even though I had it off for most of that. Is this normal?

To deal with the heat, I had to install a custom kernel and undervolt/underclock a bit. Before flashing, I noticed this thing is forcing itself to max frequency (1.7 GHz) which explains the heat. So the battery is draining because of this, presumably. I switched to intellidemand and lowered the clock a bit so it can last 12 hours (Doing nothing at all) instead, but that's still horrible compared to what I had before I sent it in.

Before I sent my phone in I typically had stock kernel while using insert coin or trick, Power Saver On, Auto-Sync Off, All Play Services/Google Now On and got 4-5 hours OST. Now I can barely get 2 hours.

Does anyone know where I can look to find the cause of my processor forcing itself to max frequency? I want to figure this out before I annoyingly have to send it in again. (Have to S-On/Re-Lock again =\)I was thinking maybe something shorted when they replaced the camera.
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