Hi Paul, I've just checked my kit.
1. The spirit level is not the best and I think you know it's used by looking through the viewfinder. And while it works, It's limited in its movement. Try slightly exaggerated tilts to see if you can perceive any movement of the bubble as you look through the viewfinder.
2. My viewfinder is also extremely clean and there is some flare but nothing too distracting. I have more issues at the eye end and maybe this is what you mean, when the lines ghost? This too, I believe is normal, happens with many RF's. It helps to adjust the diopter, pull out the eye cup, keep a little distance and shield if necessary. Fortunately, it's only for 'rough' composition and not for focus.
3. All my lenses rattle, you'll be pleased to know! Perhaps some more than others. I don't know what it is, they all worked fine the last time I used them which was admittedly quite a while a go.
It's a fabulous outfit, enjoy using it!