Changed clutch now knocking
 

I have a 2000 mustang GT that is supercharged. My throw out was going bad so I decided to just change out the clutch while I did it. I changed the clutch and throw out bearing but nothing else, the flywheel looked fine along with the pilot bearing so I checked everything and it looked ok. Now after I have put it all back together except 2 of my o2 sensors connected to the exhaust close to the headers ( because the passenger side exhaust pipe threads are stripped in the pipe). It is making a knocking noise kindve sounding like metal tapping metal and when I push the clutch in the noise gets quieter. It also is harder to put in gear and whenever I did a test drive every time I shifted the rpms would stay and go up it would act like I was tapping on the gas. But I haven't figured out how to get rid of any of these problems after looking it over any help would be much appreciated.