The patience, flexibility and willingness of Long Island Rail Road commuters to try new ways of getting to and from work will be tested when Amtrak’s emergency repairs at Penn Station begin July 10. The summer of disruption will be tough for all riders on the nation’s busiest commuter railroad, which boasts an average weekday ridership of more than 300,000.

The Metropolitan Transportation Authority’s contingency plans to mitigate the pain are extensive, dare we say forward looking, as the agency encourages those who ride the rails and drive cars and trucks to think differently about their travels to and from Manhattan.

But it won’t be easy. The MTA will have to cut LIRR service by 13 percent for an expected eight weeks, canceling some trains and diverting others. The MTA will add cars to trains, and three trains each weekday, and provide free transfers to the subways at Jamaica, Hunterspoint Avenue and Atlantic Terminal. Manhattan-bound commuters also will be able to carpool or take one of 200 coach buses from new park-and-ride points, or take ferries from Glen Cove and a yet-to-be-determined South Shore port.

Meanwhile, the MTA will cancel three overnight trains each night to prepare for the morning rush. That’s necessary because the Island lacks the ability to position trains and keep both tracks in use on its Main Line. In this crisis, it’s worth remembering that the proposed all-important third track on the Main Line would solve this in the future. State senators who won’t be part of the solution will be blamed.

Knowing that more commuters will drive, Gov. Andrew M. Cuomo announced plans Monday to complete construction on East River bridges and tunnels before train service is reduced. And, in one of the more exciting pieces of the MTA’s plan, truck drivers will pay a 50 percent lower toll to Manhattan if they enter between 10 p.m. and 5 a.m. It’s an experiment with congestion pricing, and a good start.

It all sounds promising, yet such plans often don’t work out. After all, we are talking about the LIRR and the MTA, moribund bureaucracies trapped inside a feudal system that can be challenged by a heavy rain.

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There are many questions. Where will the South Shore ferry be located? Can New York City accommodate the 200 express buses in the Queens high occupancy vehicle lane lane that feeds into the Midtown Tunnel? Can it increase enforcement of bus-only lanes on 34th and 42nd streets? How will the beleaguered and overcrowded subways deal with more riders? And, of course, who will pay for all this mishegoss that Amtrak has caused? The MTA has no margin for error. It must execute its plans with precision and care. Agency executives must be flexible and quick to respond when there are problems. Above all, they have to COMMUNICATE with commuters better than ever before.

Out of this summer of pain might come creative ways to change how we commute on the rails, roads and waterways. And this is a sharp reminder that we need leadership and action to maintain and upgrade our region’s transportation infrastructure so we don’t find ourselves sidelined again. — The editorial board