If a shop installed the cranks/BB for you then, yes I would take it back in. Never had a problem with Sugino75 stuff and always got a near perfect chainline (have switched away from the S75 BBs to cheap-o campy sealed BBs which throw your chainline off by a 1mm).

If the ring looks warped I wonder if its not sitting on the spider correctly due to a burr or just needing a little tap to seat itself correctly. Either way your mechanic should be able to diagnose correctly.

Removing the bearings from the retainers shouldn't cause any real issues and you should get a smoother running BB. Retainers are there solely for convenience of maintenance/install (much easier to deal with retainers than 20+ individual bearings). Your BB may just be a little too tight which would make it appear noisey.

Sorry for your frustrating experience.