You simple select the sh.. and try to run a Fillet on it. ;-)
If it doesn't disappear in a mess of broken curves and strange naked rectangular surfaces - try running Boolean trim on it.
I believe that the remedy for the pinching on the ends can be addressed in the same manner that Michael suggested for smoothing out the creasing that can occur as the rails approach the (polar) middle-end point.
- By placing a small circle or some smaller profile rings to express and reinforce the shape in those areas.
Or in other words, if a small profile ring of a more round and smooth shape was placed where it really looks creased, it may smooth it out there and lessen the overall extremeness of the pinching.