what are the two holes in the bottom of the box for? There is one just behind the TB and one by the passenger side runner holes. Do these need to be plugged? I had plugs in there but lost one when I took them out to powder coat. Should I use loctite if I put them back in?

 

I've got the plugs in mine (of course, I also don't have an EGR since the heads aren't drilled for it and I don't have the 9th cold start injector). Call LPE and ask them if/when those should be plugged or left open. I got mine used so no info was available on that, and the directions I pulled off the LPE website says to install the plugs.

 

The one by the plenum is for the IAT IIRC. The rear, does it have a snout (brake booster)? It should be plugged if not in use though, because otherwise it will be unmetered air, and that would sufficiently **** off your ECM.