Not to sound too cavalier, but while I have experienced all the things you mentioned (other than the aggressive drivers in MO), I have not found any to be unmanageable. We just rode every day, mostly stayed on the AC route and found it fine. Of the things you mention the winds in KS were the worst, but the only thing you can really do about that is to try to get in as much of your mileage as you can as early in the day as you can.
You mention talking to locals about the best roads... I will caution you that most of the locals I have encountered while well intentioned gave horrible route advice. It was hard to believe that they had even seen the roads when what we encountered was so far from what they described. I did find that big rig truckers were an exception as were some of the farmers.
The average car driver might say something like "It is exactly 20 miles to X, there is a good shoulder, and it is mostly flat or downhill". When we would ride it it would be 32 miles mostly uphill and no or unrideable shoulder.
A trucker might say something like "don't hold me to this, but I think it is about 32.2 miles, mostly no rideable shoulder, and it starts out flat for about 5 miles and the gradually climbs for the next 25 miles, before descending into X". When we would ride it we would find the description to be spot on.
We did take alternate routes rather than stay with the AC route sometimes mostly to take a more direct or flatter route, but never to avoid traffic.