Well, as far as physical connections, I've got the flapper welded onto the bulkhead via a single coupler - let's say there are maybe 3" of space in there with perhaps a 1.5" inside diameter. Then it runs down about 6", hits an elbow, travels another 12" to the corner (I should have planned the bloody thing to account for the lighting! Now I have to bypass around it!), and down the final 6" or so. The outlet itself is a 90 degree elbow so it's parallel to the water surface but submerged at all times. Another guy on RC I was talking to was having huge problems with the flapper closing but it ended up being caused by his outlet being above the surface.
Here's a shot from a little farther back about a week into the cycle...
Bubbles? There are a lot, but I've stopped caring about them so much now that I found a good position for the powerhead to deflect them off the corals. Once the surge has begun no new air siphons in, so it becomes a "clean" surge after that.
If bubbles are your enemy, there are 2 options.. Solenoid (the clicky would annoy me more in the night than the gush of bubbly water, somehow), or a vacuum design. I'm subscribed to an RC thread somewhere where a guy actually built a chamber within his surge chamber to control the air and the end result is no bubbles! I've read it a couple times and never been in a temper to fully understand it, but I'll dig up the link after/at work today.
One thing with the Borneman, however, is that you NEED to guarantee a minimum rise of water level in the surge tank. If it's too slow you *will* end up with a flapper slightly starting to open, then water draining and the whole contraption closing down again.. Water level rises a bit again.. Flapper lifts slightly.. Yeah.