If the above question wrt a high spot in the middle of the lower intake is the issue, I've noted this warp a few times. It's common on 3.0L engines and can be resolved by milling the lower intake head flanges. I have pictures on my home PC, but no access to them now.

You can check the flanges with a straightedge or on a flat surface like a kitchen countertop. If the lower intake is badly warped, it should also be checked to make certain the top flange is straight..... it may need to be milled also.

The first thing to do is to see what's warped - heads or lower intake. Also, make sure that the lower intake stud threads will allow full torque-down of the nuts..... if not, an extra washer can be used to take up slack. Also, tighten the nuts as you would a head bolt sequence, starting in the middle of the stud pattern and working in a circle toward the ends in steps of increasing torque value until you reach the prescribed limit.

Finally, I would suggest using Permatex Copper Spray-A-Gasket.... 2 coats on the head flanges, gaskets (both sides) and the lower intake flanges.

Frank