[For the last 15 years or so I have always used the Sapim Polyax nipples for my builds. They may not always be necessary, but they don't do any harm and are cheap enough. 

Rohloff spokes have always come with Polyax nipples, though they've recently changed to the new locking version, which is still Polyax.  They're an interesting idea, I think it deforms the thread, it seems mainly an advantage for machine built wheels, they're also aluminium which puts me off. 

I noticed over the years that in Europe Sapim spokes and their Polyax nipples are almost a default choice on serious bikes (as distinct from bike-profile objects sold by supermarkets), with the closest competition coming from DT Swiss. In the States, Wheelsmith spokes are mentioned so often, one can be excused for thinking they are the only spokes available, which of course is unlikely.

I just wish the Sapim Strong spokes, as for instance fitted to my Utopia-velo Kranich, were not so butt-ugly, not to mince any words about their in-your-face butts. I suspect the butts of the Sapim Strong, or anyway of the special Rohloff version*, were not made more aesthetically pleasing by blending the extra-thick butt into the long middle section because of a misplaced aversion to even a micro-gramme of extra weight. There's no complaint with the way the Sapim Strong do what it says on the tin: my wheels are as tight and as straight as on the day the bike arrived fifteen-odd years ago in contrast to a bike from the reputable Royal Dutch Gazelle factory which arrived with spoke tension all over the dial in wheels I virtually had to rebuild if I wanted them to last.

* As far as I know, the special Rohloff version Sapim Strong spokes are different mainly or even solely in the angle at the hub end to preserve the flange. Correction welcome if you know better.

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I have built probably over 100 wheels, but only one with a Speedhub. For the last 15 years or so I have always used the Sapim Polyax nipples for my builds. They may not always be necessary, but they don't do any harm and are cheap enough. I don't always use Sapim spokes, sometimes the right length wasn't available with Sapim so I used another brand, generally DT Swiss.

That is a lot more than I have built, but I built all the wheels on my bikes with the exception of my road bike that I bought as a complete bike.  That said, I did build a dynohub wheel for that road bike, so I am only using one wheel that I did not build.

I used Wheelsmith spokes and I am not sure which brand of nipples I used until I built my Rohloff wheel in 2013.  I bought the Polyax nipples for that wheel, and have used them since for all of my wheels.  And my most recent wheel, the Wheelsmith spokes were unavailable, I used Sapim spokes.

I suspect that SJS uses Sapim nipples and spokes, but do not know with certainty.

I used Sapim Polyax nipples and Wheelsmith spokes on my Nomad Mk II, but Wheelsmith (no longer in business) made the spokes about 90 miles from my home, so I had some local bias.

It's not too clear from your photographs but it looks as though the hoop is secured with P clips, and it may be wrongly assembled.

Is it possible to completely removed the hoop and swap the two pannier supports left to right. You should then be able to refit the hoop on the outside of the pannier supports.