I'm sorry to hear of your paint troubles.
I'm not too sure what you mean by 'visual ridges', but it doesn't surprise me that you can see a difference between where the stripe was and wasn't. The UV component of daylight will have caused a small amount of degradation to some of the pigments in the paint and since the human eye is very sensitive to small differences in colour, you will see a stripe effect. Boundary effects are always going to be the most noticeable.
Its probably not too much to worry about though since the part which was under the stripe will now start to fade, given a few months (not sure what the weather is like in Kansas) the stripe effect will probably have vanished. If it never goes (and I guess you'll always know where to look) you could also apply the bonnet stripes back again! I doubt polishing would have much of an effect as the fading has probably occured below the clear coat - never know though, could be worth a try if nothing else works!
As an aside point in the factory after the top clear coat is applied, the whole painted body is passed through an oven at temperatures around 120°C to fully crosslink the polymers in the clear coat. Once this is done the coating should not 'sag' or 'flow'.
I think if other people, especially those in nice sunny parts of the world, removed their stripes they would see something very similar. (and probably a lot worse for the older cars
)