Need help with 2 vacuum lines

So I seem to be missing a couple small vacuum lines. I have downloaded the FSM and tried googling but I just can't find a good clear picture to figure out what is what. So I figured I'd turn to you guys!

The one ontop of the plenum looks like there should be a hose connected to both ends, but to/from what?
The one on the bottom definitely has suction, but what does it run to? I have a bad misfire on 3 and 5 and hoping this might fix it!

Thanks guys!

 

Extra tube used for other emmision requirements. Mine is like yours.
That's not causing your misfire.

 

The 90 degree piece on the back side of the upper intake plenum needs to be capped. leaving it uncapped would allow for un-metered air into the engine and it also looks like the larger vacuum hose on top of the plenum needs to be replaced due to the amount of cracks on the throttle body side.

 

Correct vac line routing is on sticker under the hood

 

https://www.tacomaworld.com/threads/random-tubing-on-5vz-fe.298430/

first pic is 03-04 electronic TB, like yours. cap that 90° facing up

 

also, a vacuum leak like one caused by that small 90 degree elbow would throw a random misfire code, P0300. Cylinders 3 and 5 are neighboring cylinders and that’s not good. Now, it could be that you have two bad coil packs or spark plugs, or a combination of both, but I highly recommend you troubleshoot for a bad head gasket or take it to a shop if you don’t know how. How’s your coolant level?