Q: Could i have caused an engine modulation?

I have a 2002 ford Taurus with the 3.0 L OHV. I recently replaced the ignition coil, spark plugs, and plug wires and the car runs great. However, i noticed that since i replaced those parts, i have a very heavy "modulation", or pulsing in my engine. I am very in tuned with my car and i notice the smallest changes. So this is making me nervous. Is this something i need to worry about? I fear i may have accidentally damaged my motor, since we managed to cross 2 spark plug wires and my motor was not firing in the correct order. (2 people trying to work on the motor at once and 3 wires ended up being pulled completely off at once) Would this cause damage that may explain the sudden pulsing tone? If it matters, we crossed cylinder 4 and 5, so as the firing order, it was causing my 6th cylinder to fire on 4, instead of 5, and my 4th cylinder was firing on 5 instead of 4.

My car has 201142 miles.
My car has an automatic transmission.