You are quite correct in your findings; they do clash horribly. I came to the conclusion that the O2's mechanical linkage to the draincocks was dreadful; I think Don Young mentions somewhere (I can't find it in his ME articles) that the full-sized linkages were a nightmare, so reducing the size of it by a factor of 12 looks like sheer stupidity! Same goes for the sanding; I've just made the visible bit over the front splashers. Not a good idea to have sand on small locos in my opinion.
To that end I've made some automatic Bill van Brocklin type drain cocks for mine. In which respect I pondered for some time whether the business part of the draincocks should be level or be made parallel to the inclined cylinders. Level won, so that's how I made them, but whether they work or not is still a question for the future.
Another option would be steam-operated drains; there have been several ideas published on designs of this in ME. It can be a lot easier to route bits of pipe than mechanical linkages.
I've also made my bunker into an extra water tank, with suitable balance pipes under the footplate. This obviates the need for that strange cross-pipe affair just behind the backhead.