[Rick Parker]

A couple of suggestions: When the pressure plate is tightend down to the flywheel, be sure and remove the little wooden/plastic blocks that hold the release levers from hitting on the pressure plate itself, they are installed during manufacture, in your picture they still appear to be in place. Are you using an OEM engine plate? The aftermarket ones are thicker by approx .070.
As said previously be sure clutch disc has correct side toward engine. Once you have verified that parts are correctly oriented take a few measurements and it is a real simple job to shorten the bearing retainer. It's only functions are to obviously retain the input bearing but secondly to provide a surface for the throw-out bearing to slide on. If it actually needed to be shortened a minor amount I would not anticipate any problems in doing it.
Have you used an alignment tool while installing the disc & pressure plate? Measure carefully before machining. Use Vernier Calipers, or depth gauges.

Rick