Crankcase ventilation thap pipe probably is. You can keep it blocked up, unless you want to run a normal PCV valve back to the inlet manifold, for polution reasons. Just make sure the vent on top of the cam cover is vented somewhere and not blocked. You can either put a filter on it, or just have a hose going back behind the engine facing the ground. Or you can have the top hose going to a catch can, and another hose to the catch can from the crank plate vent if you want.
The big bumps in the floor of the exhaust ports, are ment to be there. But no one knows why. It is solid aluminium though and when porting those heads, people grind them down flush.
Issues with extracters will depend on the brand. Do what you think is right.