The top flange (8") on the collection cup hits the injection tube and keeps it from lining up with the hole in the top of the box. I can probabily just make a new top and space the 2 tubes farther apart.
I'm also wondering if the top is thick enough. It is 1/4" acrylic. It looks like it bows down abit from the weight of the riser and injection tubes. but, that could be because the top is not glued in place yet.

It should stiffen it up when it is glued on all 4 sides.