1995 Ford Taurus popping noise after tune up

1995 Ford Taurus SHO mileage: 93,000. I changed my plugs and wires the other day and found that an old wire boot had decayed and broken apart in my plug well. I fished most of it out but a good-sized piece (1/2") fell into the cylinder. With the new plugs and wires, I started it up to find a "popping" from the engine and exhaust. I checked and re-gapped the plugs and the idle was fine. As soon as I put it into gear the "popping" returned. When I open up the throttle, I don't hear it but it returns at stoplights. There is a slight loss in power off the blocks. Is it that stupid rubber boot piece or some misfire that I can't spot? If my wires were crossed from ignition box to plug, would that be a cause also?