What is your current WMS-WMS? You could put a later axle in to get the wheels at the right width without using spacers or extensions.
My personal opinion is that trying to raise it enough to clear will look worse than either tubbing it or widening the axle. That comes down to personal preference though.
It is fairly common to have raised bed floors on conversions to newer frames, but I have never really liked that look myself.
What other modifications are you doing to the truck? Any drivetrain/suspension changes? If so, those could inform better advice.
