If only the plugs are in the wrong spot, it shouldn't be that big of a deal. Now if the T1 wire was going to the L1 plug, you'd have problems. There are lots of things that could cause vibrations on the car, U joints are one of them. If you were doing some hard launches with a 6 puck clutch, I could see that damaging your U joints. But the vibration could be caused by wheels being out of balance or an air bubble in the tire. You should try to find a Walbro 255 lph fuel pump ($115) to help raise your fuel pressure, that should help. How big is your down pipe? 2.5"? Reactive mufflers are just universal "ricer fart cans" right? Is the car pretty loud with them on there?