What is causing engine cover not fitting properly

Hey, I just bought a 2006 DCSB tacoma with the 4.0 v6. My engine cover is only held down by the driver side and the bolt that suppose to stick up through the hole on the passenger side is about 2-3 inches too far over. I was very confused about it so I took some pics to see what y'all thought about why it is like this. There is another bracket on down below the air filter box that is also 2-3 inches over from where it should be bolted into place. I noticed a 2 inch aluminum spacer looking piece near the front where air goes in the engine. What is that?

 

Looks like a throttle body spacer

 

Welcome to TW! I think it is what Supra suggested .

 

Yep and yep. Just lose both the spacer and the cover. Neither one does anything.

 

I'd also suggest removing the spacer as they are just an expensive paper weight. I'd put the cover back on as it looks nicer than the crap underneath it.

 

Yea I like things the original factory way. What is the purpose of it?

 

Spacer: cool whistle noise.

Cover: covers.

 

I removed the spacer a few days ago and also replaced the old k&n filter that was in it with just a generic filter. Just today I got a check engine code p0606 come up. Could removing that caused this? Or is this something completely different? Any advice is appreciated.

 

Did you disconnect your battery?

 

No