If the head is still off the car you need to pull the cam out of the head and place the head upside down on a table. Make sure it is level and fill the combustion cambers with water. Wait a little and see if any water has leaked out of any and into the intake runners. This will let you know if you have a leaky intake valve. I have seen were carbon will cause a leak.

However, I don't think this is the entire problem with why it won't run but I may explain the air in intake manifold. Good luck.