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The aluminum skin and wings fatigue.

It's more a certain number of takeoff and landings rather than flight time. After that the metal is too weak and unsafe.

Each time the cabin pressure changes the skin moves. Each time it takes off or lands the wings flex. They probably flex during flight as well.

First link I found: http://www.economist.com/blogs/babbage/2011/04/aircraft_fati...

That still doesn't explain the low total time limit. 5000 hours is low compared to the typical 50000+ hours that modern jets are rated for.

Modern jets aren't prop-driven Soviet strategic bombers. They are typically built for comfortable, cost-effective, long-term operation, not to be a credible threat to deter (or carry out) a life-or-death war with an economically far more advanced adversary.

The maintenance service costs at that number of flight hours probably exceeds it's economic value.

Yup. It's purely badass value.

They are probably referring to the engines. Engines are rated in hours.

Probably before the next round of maintenance.