Driveability Problems

When I drive the car down the road it kind of stumbles and the RPM's go down around 500 or so and then I give it gas and it seems like it has no performance. Then it kind of sputters out and kicks and jumps for a second. I was thinking a plug or wire but they were changed using Motorcraft. Timing is correct and Cap and rotor look fine. Also, when it sputters and kicks, black smoke comes out and a lot of it. So its running rich for some reason. It all started doing this after I put a different tranny in it. Clutch and shifting are fine now but performance is down. It also runs kind of rough too. There are a lot of symptoms so I would appreciate it if someone responded. Thanks
 
Here's the things that I would do first:

- Pull your plugs and take a look at them.
Check for fouling.
- Check your timing once more.
- 02 sensor if you say its running rich.
- Make sure plug wires are properly
connected.
- I might try some injector cleaner or
something. It sounds like you may have
a fuel problem.
- Fuel filter

Thats about all I can think of right now. It's late and Im not that bright to begin with.