Instead of setting up tolls for commuters raise the taxes for those businesses that cause the problem: they are an "attractive nuisance" in zoning terms.
Instead of buildin "high-volume transit stations with adequate parking could be placed along major highways, especially closer to remote suburbs where traffic enters the funnel" and then operating an enormously expensive transit system, why not just put the office buildings at those locations you suggest, with adequate parking.
For what it costs to operate the transit system you could give the office space away for free, and with the offices where the parking is you would already be at work so the transit system would be unnecessary. Just think of the resources and wasted time you could save.