Clutch noise after ConFE/1.375 input shaft install

[Jerred]

I just installed a new SB 13" ConFE 1.375 and the bigger 1.375" input shaft. Immediately after the install, something is making a "zinging" noise upon every shift. I suspected it was the input shaft as I had to install it with a paper shim in between the input shaft bearing retainer and the bellhousing. Without the shim, the shaft would not turn with the four bolts torqued down. I called SB and they thought it was a tranny shim problem.

I took the truck to a local diesel shop (very well respected and capable) and they tore it all appart and inspected my work. Turns out, the input shaft bearing was not pressed on far enough. They fixed it and reinstalled. They also inspected the rest of my work and said it was good to go.

Well, the noise is still there. The clutch also seems to let out very near the floor. I damn near have to push the pedal into the engine compartment to get it to release. Double clutching seems to help a bit, but the noise is still there on every shift. I also get the noise at highway speed when I let off the throttle a bit to coast while maintaining light throttle.

I don't think it's tranny related as I did nothing to it on the clutch install. I know the clutch has to break in a little and that the pedal will eventually return to near stock feel/operation. Anyone have any ideas about the noise? Possibly the throwout bearing?