DB,
The only thing that led me away from thinking about amp tuning and harmonic content was that groundwire stated that he gets a 1.6 SWR when running the Yaesu right to the antenna.
If we trust that the SWR meter being used isn't itself part of the problem, then this leads me to an antenna installation issue, or more likely a grounding issue.
Yeah, at this point i am just guessing.
If it were my vehicle i would do a quick test to help isolate this possible problem.
take that yaesu out of the vehicle, put it on a table right outside of it, and power the yaesu with an external power supply that has zero connections to the vehicle.
this ensures that your vehicle is nothing more than one antenna and whatever groundplane you have made for it by bonding your vehicle together.
the radio's only connection with this system is the coaxial cable that goes from the radio to the antenna through an SWR meter (make sure that SWR meter isn't touching any metal in the vehicle just to be sure).
if testing with the radio isolated from the vehicle produces a lower SWR, then this would point to some sort of grounding issue between the way the radio is installed in the vehicle and the grounding of the antenna.
LC