Those other holes in the VC are for the PCV system. Get a Chiltons or other shop manual for routing and other information. The other is for the heat riser off the exhaust manifold to help the engine warm up faster. Not generally needed. The theory is that cold engines put out a lot more emissions due to running rich. The faster the engine warms up, the better.
1986 CJ7, 4.2 w/4.0 head, TFI-HEI hybrid ignition, Clifford manifold w/Holley 390 w/cold air intake, OBA (in work), 150 amp alt., 4.5" lift, Woody CV shaft, 4.10 gears - lunchbox in front, Truetrac in the back, twin-sticked, blower upgrade for running topless, keepin' it simple.
It's just a Jeep, and if you don't wheel it once in a while, it's not even that.