Bulkheads - your choice slip vs. threaded. I like slip on the inside and threaded on the outside. Inside the box - use slip fittings and don't glue. None of these joints need to be 100% watertight, and doing it this way means you can pull it apart easily.
Outside the tank - it's really personal preference and will depend on what you want to use to get the water to the sump. You could thread/glue a nipple on and just use soft vinyl hose or corrugated hose. Or you could hard-plumb with PVC. Or use flex PVC. Whatever you choose, just be sure you're installing it appropriately for the given material.
You don't need 6 inches between the two drains - you really only need enough to keep the bottom drain submerged (not sucking air) while the top drain is still JUST above the water level. It's probably more like 2 inches in most setups (Assuming the siphon drain is a downward facing opening, i.e. an elbow pointing down). The extra height is nice because it gives you more wiggle room when adjusting the siphon valve but it is not a requirement.
The emergency should always be at least as big as the siphon - if the emergency is smaller, it might not be able to handle the full flow if the siphon gets plugged.
If you want to use a smaller box, it's typical to put the bulkheads in the side/back of the tank and build a small box around them. Then, you use a downturned elbow on the full siphon (so the opening is down near the bottom of the box) and an upturned elbow on the emergency (so the opening is up near the surface).