Timing belt jumped a tooth? Not likely. I don't think this happens near as often as people seem to think.
Bad EGR modulator? Not likely. Pretty simple and basic device.
What it could be is a restricted/clogged EGR passage. The EGR passages are known for getting restricted/clogged. There is an external metal tube on the passengers side of the engine, a passage internal to the back of the head that runs from the exhaust manifold over to the EGR valve, and a passage from the EGR valve to the intake area that all usually cause problems. You can clean them with aerosol brake cleaner and a stiff wire or old speedo cable, and compressed air. It usually takes a lot of spraying, jabbing/poking and air to get the passages throughly clean. Also, the EGR valve itself can get build up in it and need cleaned.
One way to isolate which cylinder is missing is to pull the spark plugs wires, one at a time, then reconnect. When the engine runs the same with a particular wire disconnected, then you have found the cylinder with the issue. It could be a spark plug, a wire, the distributor or the piston/rings/cylinder itself. Usually, it is a faulty plug or wire.