That modification is good. Leave the belly of the manifold alone. Some have smoothed out the ribbing in it and found that it diminished performance. Though they're very rough and crude looking, they help with the flow of air/fuel. To take maximum advantage of your modification you'll need to bore the throttle body, maybe even add a spacer, too.
The PCV port that goes into the snorkel must be outside the intake, else you have an open port with unmetered air being pulled into the intake.