Ford: 1999 Cobra, clutch plate, o2 sensors

Question
Yes I am a woman & I know somewhat of what I am trying to explain to you, so just try to bare with me please!  I recently purchased a 1999 supercharged (vortech) cobra from a friend.  We took it knowing it had a slight rattle.  The rattle occurs at the top of each gear except for 5th.  I know this is a good car.  Everything that has been added to this car was done right (meaning this wasn't a 17 year old kid trying to make it faster, this was a man that knew what he was doing).  Anyway, when asking others what they thought the problem was, we heard: pilot barring, throwout barring, clutch plate & that the timing chain was hitting something (can't remember what they told me).  My husband pulled the transmission & discoved that it wasn't the clutch plate, but still changed the pilot barring & throwout barring.  After those were replaced and the transmission was put back in, we took it down the road to see if we could still hear the rattle.  It was still there, but the car still drove fine just as it always has.  My husband then took his dad down the road without me in the car.  He shifted into 2nd, heard a loud "noise", lost a good bit of power & the speedometer now doesn't work, it also began to backfire but just every so often.  My husband reset the computer and some of the power was restored.  My dad (who is pretty knowledable about Fords/Mustangs) said it could be the o2 sensors.  

So I am asking your opinion?! Please help!

Answer
Were you able to get any of the codes out of the computer before the reset was done? I think they were talking bout the timing chain tensioners... being that it sounds like the noise is rpm related and not mph related it is most likley not in the transmisson. How many miles on the car? if you can try to get some check engine codes we can go alot further with this... (And I am glad to see that a woman is trying to get her car fixed without relying on someone to do it for her... :)    )