on your M104 the ECU will shut down a cylinder pair if it detects a misfire on one/both of the cylinders. There is a possibility the 3 second wait is the time required for the ECU to perform the detection. The rough running is after the cylinders are deactivated. Shutting down a cylinder pair is setting the code 23.

Swap the coil packs around and see if the fault moves to a different cylinder pair. If so, you almost certainly have a bad coil. If the fault does not move, look elsewhere.

The exhaust smell is likely from dumping a bunch of raw gasoline into the exhaust from the misfiring cylinder(s) before they get shut off.

All the symptoms hang together and point toward a single bad coil.