I'd check that the aperture stop down lever is moving fully, you can check the full movement by doing a stop down/ mirror lock-up sequence. One of the 3 or 4 motors in an F4 moves this lever, and shares duty with shutter charging. Its my theory that as either the motor wears or as other parts wear or stick then this lever motion isn't complete, which then can cause the lens to not fully stop down.
I am not 100% sure, but I believe in the case of P and S modes, the lens is precisely stopped down by this lever movement, (which is what the Ai-S series lenses do different than Ai or the F and K do, a linear stop-down lever movement).
(Which *may not* apply in your case).
I have 2 F4s that are doing this.