Quick update...the silicone on the caps works brilliantly. Still not sure about how I'm going to fix the secondary drain air line in place...one item off the list, one item on the list.
Also confirmed that even if the return bulkheads fail (the ones in the overflow box) and the tank drains below that level, the sump water levels are okay. This should 'in theory' mean that if the ball check-valves stick open, there should be just enough space to accommodate whatever siphons out. I think I might 'arch' the flex line and drill a hole just in case.
One other note on check valves...they rattle...a lot. That is unfortunate. Even more so that I have already glued them in place.