I think while you are being cautious is good, you are overworrying this a bit.
The vast vast majority of state and US highways are designed and made for tractor trailers which means you will have no problem. The very few that are not are well marked. But as the driver it's your job to know the height of your vehicle and pay attention.
Even most lesser roads like county roads will be perfectly ok.
The Commercial Drivers version of the Rand Mc Nalley Road atlas has all approved truck acceptable roads outlined in yellow. I personally would never rely solely on GPS. While they are a great tool, they are not accurate enough for you to leave the decision about low bridges to them.
About low bridges. The overwhelming majority of low bridges, which are individually listed in the Road Atlas above, are clustered East of the Miss. River and then mostly in the far east of the country. Chicago being a big example in the midwest, But most exist in downtown areas. or on small country roads that are well signed for trucks.
I would not "plan" any trip to this detail myself.
As for small towns and cities they all accommodate trucks, buses, and tractor trailers so the chance of you having a real problem is small.
My advice, drop all the minute detail planning and worry, set a route that uses State and US highways and interstates and GO.
You will be just fine.