My 16 year old daughter purchased an 03 civic lx automatic with 178k miles a couple months ago. Previous owners said they just replaced the timing belt and water pump. I test drove it about 10-15 minutes and everything checked out fine. Fast forward to about a month ago and the first time the cars been driven over 15-20 minutes straight it overheats on the Interstate on my daughter, I get it towed home and I ended up replacing the head gasket, I go on and put a new timing belt on it as well just so I know it's new, car runs fine. A couple weeks later, which is now last week she calls me and says the cel is on and its jerking/bucking . She drives it home and that's where I am today with it.

I started it last night and went to pull it in the garage, noticed the lights are flickering a bit, not sure if it's related but wanted to mention it. I pulled the codes and it's pointing to the crankshaft position sensor but before I rip it back down again I wanted make sure I was on the right path. Here's a screen shot of the codes, the pending ones I believe are related to the first fault code as I pulled them several other times and only the fault code shows. I did clear the code and the car then drove fine for a bit and a few minutes later right back to where it was. CEL on, bucking and won't rev past about 3.5k

Disconnect and look closely, see if the terminals in the sensor and inside the wiring connector show any signs of corrosion and/or liquid contamination.
If not, probably replace the CKP sensor.

I did, and that I can tell they are clean. Looks like someone used some dielectric grease at some point.