I too have a '94 YJ SE 4.0. It has a tap that sounds like a valve tap since day one. I remember back in the usenet days, there were many discussions about this in the jeep groups. I've learned to ignore this tap, and I have 112,000+ miles on mine and still running strong. If your power and mileage are strong, your fluids look good, and the engine revs smoothly, learn to live with this.
I've noticed over the years that I often hear "new" noises while driving. Often these noises are not present or noticeable the next time I'm at the wheel. My advice, turn up the music.