Cap- Like most design questions, there is no hard answer. It all needs to balance out, so it's hard to give a number. For my uses, I leave at least 1' between the inside tube and the neck of the skimmer. That seams to work fine.
For the exit bulkhead, you can use a 1.5" ell inside the box, to pull the water from the bottom of the box. In reality it does not do much though, so don't worry if you can't fit it in.
For the baffles, there is just one main baffle to help direct the input water up the tube. In practice the air in the input water really wants to rise up the tube, and it pulls the water with it, so you don't need much of a baffle to get it moving where you want it.
Zeph