Hey John,
I mostly agree with ivans detailed assesment. However, I think that the detail in the pipes shown in the close up should be able to get you something at least, if not perfect of course. Missing parts of the pipes point to a problem of alignment in this area.
Have you tried exif grouping yet? As a general rule, if you are trying to improve alignments you need to delete the flawed components because otherwise RC will use those as a starting point.
Using Control Points might also help a great deal - I managed to get some cables on a wall modelled by doing that. They don’t have to be on the pipe directly, just in the vincinity to help the alignment along.
I am wondering about the orange lines between some of the cameras in one of your screenshots. Is it possible that this is due to GPS coordinates? Because those have been known to cause trouble sometimes, so you might want to consider switching it off or deleting the data from exif (only in copies, naturally).