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The trains may have trouble running out of Penn Station because the long tunnels require electric trains and prohibit diesels, but east of Sunnyside and Jaimaca they can use diesels to pull the trains. Setup generators at a few key fueling stations to keep the shuttles running. Don't they have a contingency plan for such an evacuation?

You're not taking into account all the electric trains sitting dead on the tracks they need to pass, like the one I was evacuated from.

Yes, but by now they should have been able to clear at least a single-track by using diesels to move those dead trains to sidings or a second mainline track. I used to be a freight conductor working out of Secaucus and Newark, so got the opportunity to learn a good bit about the rail infrastructure in the metro. However perhaps many of these stranded passengers are Amtrak riders, and Amtrak would have to borrow diesels from NJ Transit, the freight railroads, or bring them in from Philly and DC. Amtrak resources are stretched so thin that service interruptions are magnified for them.