my engine bay has been getting REALLY hot, so I took the heat shield off to look for the cause. Between cylinders 1&2 and 3&4, there are gaps at the top of the gasket, where it has two extra holes. What are those for and could they be the cause?

 

i don't see any extra holes, but the gaps are telling that your cylinder head is warped, probably due to the overheating.

 

 

Like Eran, I first thought the yellow arrows were pointing to the head gasket is located, but that is not correct.

The yellow arrows are pointing to where the exhaust manifold gasket seals to the cylinder head. It looks like you will need to replace the exhaust manifold gasket. You may have to clean where the gasket seats on the exhaust manifold and the cylinder head to make sure the gasket sits flat between them. I'd use a blue scotch pad that you get at the grocery store that is safe on glass. Nothing too abrasive. Some very fine sand paper with a flat sanding block, say 1000 grit or greater.

 

I have to ask what is too hot?? How hot is it outside? Have you been using the AC a lot? These things all add up. If it's been hot out (90+) and you're running the AC all the time you're using the car, and you're doing a lot of driving, the engine bay WILL be hot. Sorry, but someone had to say it. Same thing happens in parts of Texas, where you see 100 days of 100*+ weather.
If you're seeing temperature gauge spikes, then you'll want to have the cooling system checked (might be due for a fluid change).
In those spots circled, you're just seeing the top of the gasket. If you don't have an exhaust leak, I wouldn't worry about it/them.