Okay so I bought my 2000 mustang back in February...it ran perfectly for about 2 weeks then the transmission went out and since then it has felt like its had a miss, and there is a really rough vibration/shuttering all the time, even at an idle. So this is what has been done to the car thus far:

-Replaced the transmission with a used one(had 60k on it) Mechanic went ahead and replaced all the seals before putting in..
When it was finished it felt like the car was misfiring, so I replaced the spark plugs, wires, pcv valve, and all the filters...in the meantime the driver side exhaust manifold starting leaking pretty bad & even fell off part of the way.....so I took it off, had it welded and put it back on and changed the spark plugs again...this stopped most of the problems at an idle....
I had a friend put it on computer to see about the oxygen sensor...The car gave no codes.

As of right now, the car rarely vibrates or shutters at an idle and sometimes it doesn't when driving at speeds of greater than 45-50. It is the worst when I'm taking off from an idle or when I start slowing down...The mechanic that put the tranny in said these cars tend to shutter so he had me to go and get a small red tube of this shutter stuff and that it should help. Well it hasn't, actually I'm kinda thinking it is worse now....Does anybody have any ideas? Thanks.

 

Did they swap out the flywheel when they did the trans?
There were 2 different flywheels used in 2000 - weighted/externally balance and zero balance. Use of the wrong one will give you exactly what you are describing.

 

I honestly don't know....I was told the 99 and 2000 were the only ones that would fit and the tranny that I got came out of a 99 model...I'm going to call the mechanic and see if they changed them out or not....thanks!