Weird Transmission Problems (Clutch)

[techsan]

I recently purchased an 88 lx convt. 5.0L. The entire car was 100% stock (still has air silencer) but needed a new clutch. I bought a King Cobra Kit and, after installation, there was a loud knocking sound coming from the Bell Housing. I took it back apart and found that the pressure plate was rubbing against the Bell Housing. All of the bolts were tightened to the proper torque specs, and I even ground on the Bell Housing, but the noise is still there, but a little less extreme, and it goes away entirely when i step on the clutch. The other weird problem is that now the shifter appears to be out of place in the cab. The inerior boot and cosmetic plastic cover will not fit over the Pro 5.0 Shifter, eventhough it did after the first time i dropped the tranny. There are two issues i think could be causing this: I did not put the dust cover back on the Bell Housing during either time, and the motor mounts are shot. In addition, the second time I put the tranny back in the car I was using impact wrenches instead of hand wrenches. Any suggestions would be appreciated