Well, it could be a problem somewhere along the lines in the intake system but not in the intake manifold. Bent valves on the intake which would cause a loss of compression, and especially show up in a leak down test if they were only slightly not seating.
Also, I reread your original post. It is possible that the cam timing is off due to a bad cam alignment plate. This happened on my dad's car. The car had a strange chronic problem where it would run rough and then magically be ok. It broke a few spark plugs. Ford could never figure out the problem. Finally it had a major detonation and blew apart one of the pistons on the drives side bank. This was because the cam was constantly advancing and retarding because the plate on the front where the cam keys into the plate was a defective piece and hole was widening out. Uncontrolled variable cam timing is no bueno. You would need to pull the timing cover off the front of the motor to check it so there is a lot of labor there.
Is the car still getting terrible gas mileage? Have the dealer check to make sure the ECU isn't running on limp home mode. If the ECU has really weird readings from a sensor it can go into limp mode. Limited Operation Strategy - Limp Home Mode (LOS) makes the car run like crap and can be caused by a mechanical malfunction or a bad sensor. The **** is, it doesn't always throw a check engine light. If the car is in limp home mode, it will run rich and usually get ****ty mileage. The dealer should have the car run a cylinder balance test as well as the compression test. The balance test will rotate through dropping one cylinder at a time until it has done it to all 8 and if it finds one cylinder to cause a drop in RPM outside the range it will fail that check. This could be cause by a leaking or stopped fuel injector as it does this by cutting fuel on the cylinder it is testing.
True troubleshooting is the only way to fix this issue. I really wish you the best of luck on this and hope something you find here will help you solve the problems with this car.