Factory AC removed, no heat!

The two vacuum lines at the cowl are for the climate system. One goes from the intake to the "harmonica" in the center of the dash (the lever or pushbuttons for Vent, A/C, Def) , the other comes from the harmonica to the heater control valve.

You can either by-pass the heater control valve with a single length of hose under the hood or block the valve open. IMO, the vacuum line to the "harmonica" is more critical as the vent flaps for the heater, defroster, and the A/C vents are controlled by vacuum dashpots under the dash.