Im going to route the top one coming off the intake to a nipple Ill put on the plate behind the cone filter, that went into the stock air box. Grafted that filter/plate from K&N kit, the stock airbox was cracked and trash. Eventually Ill close this area off a little maybe with some inlets on the front quarter panel.

Will it mess with the MAF sitting at an angle like that?

Im hopeing somebody can tell me where the hose that comes straight off that T on the intake is supposed to go. Also where the top smaller hose coming off the top of the passenger side valve cover is supposed to go, thats wide open now.

That little vacuum line is still looking for a home too.

You're thinking too much into this..

Any nipples coming off a vacuum tree should not be open to atmosphere. The line you want to put in to the air cleaner does just that. Leave them plugged off. I am not sure what the vacuum line goes to, or how it hooked up before; but test your heater vents and/or cruise control, if either are broken, that is probably why. If nothing is mal-functioning, then don't worry about it. Optionally you could just hook it to one of your vacuum nipples. Just need to make sure you cap off all nipples so that you don't have a vacuum leak.

What will most likely screw with your MAF is the change in air flow characteristics due to using a cone filter on the end of it.