Tacoma 3.4L V6 tech question (Cylinder head job)

Hey guys how's it going?
I apologize if this is the wrong section for this kind of post. I'm doing head gaskets on my 2004 Tacoma 3.4 V6. I aligned the crank and cam pulleys to their respective marks. After pulling the valve cover, I was looking for the marks on the cam gears under the cover. On the drivers side, there are 2 yellow marks (that aren't factory, I'm assuming?) and they line up but the factory drill marks are 180 degrees apart. On the passenger side, the yellow marks are 180 degrees apart and the factory drill marks line up. I also noted on the passenger side (where the drill marks line up) it looks like it's been getting very hot. The bearings are like a gold color while on the driver side (where the yellow marks are lined up) it is much cleaner and the bearings have a silver color to them. Something just doesn't seem normal here.

On a side note, on the passenger side where the marks are aligned there are valves being engaged while on the driver side with the yellow marks there are no valves engaged. My manual is telling me there should be no valves engaged while taking the cams out. Does any of this sound like a problem one of you guys have run into? Any insight would be greatly appreciated.
Thanks for reading.
Sam