Good chance that bypass is part of, if not all of the problem. Not needed unless there are more mods you haven't mentioned like EFI and electric fans. I'd put it back to stock and then troubleshoot. If there is a bad bulkhead connector, you can always run a parallel wire.
If you troubleshoot the way it is, you'll have to draw it out the way it is. Then you can figure it out. Same methods as Del and I have been describing, but applied to the flow paths on your car.
