You might check the adjustment of the carburetor float level. I can't remember if you have a stock carb or not. On the stock carb there is a line etched in the glass showing where the fuel level should be, if it's too low I would expect to see your problem. On the freeway the engine is not under as much load and is at constant speed, whereas around town you have to accelerate all the time and produce torque.
A problem I have is on tip-in from a stop, the engine bog and then gets going. I've identified that to be the accelerator pump. Also, my fuel filter gets clogged with rust real easily and when it's clogged it runs poorly, similar to the way you describe.
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