The petcock is supposed to be changed to manual, no vacuum operation. It's fn in ON position is to vent the belly tank to the main. In RES position the fn changes and the flow is to the BT while the bung tube acts as vent. I don't think the vacuum tube matters if you made it manual like their instructions say. However the original tank vent tube must not be kinked. Check that. Also does it flow OK with the filler cap open?
The question remains to be answered. Should the vacuum opening on the petcock be open, or capped off?
I answered it. If it doesn't matter, then it can be either connected or not since the petcock ignores it when it's been changed to manual. However if it's not connected you need to plug the line to the #6 port or you have a vacuum leak.