I don't know when IE added that part with the evap system to the install but it is very confussing and I would ignore it. I don't see how it is relevant unless you don't have a vacuum pump. Your setup does not draw vacuum from the intake manifold but instead from the vacuum pump at the brake booster.
With your setup nothing needs to be attached to the vacuum lines under the IM.
Any tips on how to get the bottom bolt in....
Hahaha that bolt is a PITA. I just used a short alan key and put my fingers through either side of middle runner and just slowly worked the bolt in with my finger tips. I was never able to find a tool that would clear the bottom of the runner.
I was worried you were going to say that haha. I was thinking of buying a cheap allen key set from the dollar store and modifying it to be super short