The engine is the stock KA24DE. Sometimes when I drive, shift into neutral, and come to a stop the idle is high. The engine will idle around 1,300 to 1,800 RPM for a varying amount of time and then it will drop back down to 800 RPM.

I'm pretty sure it has something to do with the weird noise that is seeming to come from the head.

Here is a link to a sound clip of the engine noise:
http://www.angelfire.com/daywickell/Engine.mp3
(copy and paste the link)

I started the car and let it warm up. When the engine starts to idle at 800 RPM a weird metallic rolling sound will start happening. If I rev the engine the sound will go away but once the engine is back to idle the sound will come back.

Any ideas on why I have high idle after driving and shifting into neutral or what that weird idle sound is?

 

the sound is most likely your top chain guide. you can remove it and the sound will go away. also for the idle problem check your throttle cable to see if it is sticking or binding.

 

my old SR idled high in neutral, but that was only when it was cold. after it would warm up it would stop, but i never knew what it was.

 

Turn down your IACV a tad. You may also be using an Auto ecu which idleshigher than the 5 speed manual tranny ecu's.
Also replace your timing chain guides.