The hoses from the valve cover to air cleaner and valve cover to carb are NOT part of the air pump system but part of the PCV (positive crankcase ventilation) system and should be left in place. Most aftermarket air cleaners have a provision to add a nipple to the base for the fresh air hose to the oil cap. Depending on which TYPE of Thermactor system was installed, the "internal" or "external", you'll have either one port on the end of each cylinder head to plug with the 5/8-11 threaded plugs or one adjacent to each spark plug (8 total) where the "spider" type Thermactor manifolds were attached.