The shims worked marvelously. When the frame is down the skins are flush and it opens without interfering.
So, now I have to consider, drilling out the splice plate and re-drilling it with the frame bowed up to lift the skin like the spacers are. Or just leave the spacers. If I drill out the splice plate, I'd have to make a new one with fresh holes. And I'd have to back drill from rib to plate rather than vica versa the way we did it first time. This could be tough. And I don't know if it will help. Nor do I know what other consequences this might have.
It sure looks like if I redo the splice plate and bow up the frame sides, that that will lift the skin just like my shims do and be a good solution. So I probably will redo the splice.
*** UPDATE *** I talked to Van's they said, Use the shims!! Don't redo the splice plate. And they said, "get use to using shims. There will be lots of places where you'll need to shim to adjust fit." They also said waiting to drill for the bushings until canopy is done is a good way to keep one last chance for adjustment.