Removed complete dash Ac and Heater in 90 gt 5.0 now not running right

I completely removed the whole dash because im building a custom aluminum dash. In doing so i noticed there is a black vacuum line that goes to the ac heater selector. If the knob is in the off position you would think that its the same as being capped off. Well i removed everything down to the black line itself and now my mustang runs really rough,backfires like crazy, has no power at all and check engine light keeps coming on . I tried completely capping it off,pinching the line to allow minimal air flow, took the rubber nipple off at the vacuum tree. And the same result anyone have any suggestions