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The system would NOT have toll booths. Odds are it would be something based on data collection device built in to vehicles that was secure and recorded only relevant info about road use. The collection of the road user fee could be billed or part of some kind of IRS like reporting.
The toll roads that have converted to radio based transponders would be a similar starting point, but the rates those systems get are much higher (per mile) than anything that would be needed to fairly replace the gasoline taxes. As it is now the folks that are unfortunate enough to drive vehicles that get poor fuel economy and do the majority of their driving at the times of day that roads are most crowded end up paying a greater percentage of the motor fuel tax than folks that may drive much more but are using less fuel...