I changed my alternator today on my 98 xlt explorer before I did it ran fine and now its running ruff doesn't want to shift right and stinks. what could cause it to act like that?

 

I'm sure you know that if you disconnect the battery for a long enough period of time you will lose some of the info in the vehicle's computer.
If you take it around and drive it a while it should relearn the driving habits and improve as you drive it. If you don't see any improvement let us know.
On a different note , could you tell us why you needed to repl the alt?

If it never gets any better, I would question where you obtained the alternator.

 

I got it going thanks. I had to take battery cable off and let it set for about 30 min. so computer would reset and hooked it back up and didn't have any problems after that.