Ummm …odd though ti had exploded all the parts as you said.
Regarding the tubes being inline with the sides, I had initially had them like that in one of the model I had made, but then could not get the parts inside to delete, as when I tried to delete them, it deleted that hole side panel, no just the bit inside the circle. Once I had found out about the 'Intersect with model ’ menu item I managed to get it to work, but only after pushing the sides in so the tube protruded a bit.
I am now guessing that the world ’ solid’ has a different meaning to what I imagined. I was thinking that if an item had all sides filled, then it was a solid…
I did find another tool in the menu system called "make Solid’ so i tried that and that did then produce a stl file that MakerBot App could deal with.
If I can find another day to spare I’ll try building this up again for the nth time and see if I can get it right again.
I did actually go back and re work some of the older model I had made, with the knowledge of the "interest With Model ’ menu item …and managed to get the holes to be viewable all the way through.