Hey Josh...sorry to hear you are still having problems with the clutch. I installed the flat side of the clutch disc towards the pressure plate...extended the splines so it would side to the rear and additional 1/4-3/8". I bought a new disc/pp for my rebuilt engine and the same part number clutch disc had a stencil indicating the flat side went towards the flywheel. This is exactly opposite my original disc so I just reused my original. Flat side goes towards the pressure plate!!
On your pilot bushing....pack the hole with water soaked toilet paper...use a 9/16-5/8 dowel to pack it tight....then a 3 pound hammer smartly to get the bushing out. It works better than using grease and makes less of a mess. I discovered that the pilot bushing from the major suppliers is the correct diameter to fit snug but not overtight. NAPA couldn't get within .005" and I had to turn it down. If I had tried to install it there would have been distortion from excessive hammering. Also, I sunk it 1/8" inside the crank hole.
Hope this helps.
Dave