Fix your known broken parts then see if you still have issues.

Right now you are telling us.. "my car is out of gas because I ran it dry and it won't start." Really.. you are.

That thing that you broke, which I can't quite decipher from your description (either BCA or vac port on charger) is going to cause a vacuum leak. Depending on how bad the leak is.. will depend on how badly your car runs or if at all.