87 Bonneville idles fine, runs rough

While replacing a grommet on the valve cover of my fiance's 87 Bonneville (3.8) I decided that since neither she or I had any idea when the last time the spark plugs were changed, I would change those too. Since then, the car has run terrible. It idles fine, and when in neutral it will rev with no problems, but when it gets put in drive (or reverse) I get problems with misfiring/backfiring, sudden power loss, and the car just hesitates a lot. Also, when in drive, it idles lower and rougher than it used to. It didn't do this before I changed the spark plugs.

I have tried two different sets of new plugs, checked and re-checked the gap so make sure all the plugs had the correct gap, changed the wires just in case I buggered them up when I changed the plugs, and made extra sure that I didn't somehow put the wrong wires to the wrong plugs, all with the same results. It is fine in park/neutral, but when driving, it just runs bad.

What could I have done, and what else should I check?

*Edit: Forgot to mention, I checked through old messages, and most other times this situation came up, changing the wires seemed to do the trick. It didn't work for me.

does it have any codes in it? normaly this happens if you crack a plug when installing it. look under the hood in a dark place while it's running you are looking for sparks jumping around rev it up to where it misses or get her to put it in drive and hold the brake this will give you an idea where the miss is coming from. i can't remember if this car has coil pacs or distributor if it's a coil pac spray a little water on it and see if it runs worse.