After messing around with bell siphon designs and getting mixed/poor results I stumbled upon a very simple, reliable alternative, a hose. This has the advantages of using less materials ($), taking up zero space in the grow bed, and working flawlessly for the past six weeks. Check out my video:

Once the beds are filled and functioning, if the system works the way you expect it to over the course of a summer, let us know. From experience here's what I see as being issues with your system.

Once you have nutrient in the tank (fish or additive) your clear lines will fill with algae growth. You might get a whole summer out of one set of plastic tubes but the flow will be drastically reduced.

Keeping the feed ends of the tubes inside the beds clear will be problematic. They will fill with bedding medium, roots, particulate . . . and getting to them to solve the problem will be an issue Once your flow outflow is sufficiently reduced your beds will overflow.

While the bell system may have issues, it does have the advantage of being proven. I ran my small original bed in the sun porch all last summer. I had to pull the siphon twice to cut roots away to keep it functioning. My system isn't glued, but is held together by pressure so it was easy to do. This summer I'll wrap the riser in landscape cloth to stop the root incursion. The zucchini I grew were awesome. The tomatoes I grew the year before were equally awesome.

This is the system I built about six years ago http://norisstuff.com/aquaponics/auto-siphon/. I still use it. During the summer growing season it sits over the top of a rubbermaid watering trough with nice big goldies in it. Last summer I grew zucchini and it produced them faster than I could eat them. The year before I grew tomatoes which were delish.

Thanks for the thoughts Elf Nori. You may well be right about that. After six weeks the visible tubing that supplies the top bed and the one that drains into the fish tank have algal growth. The root systems in the beds are just ramping up, and I could imagine them clogging the tubes at the end where the netting keeps the pebbles out.
I wonder if having solid color tubing would keep algal growth down. I'll have a look in the gravel and see if those tubes are cleaner than the visible ones.
Mark

You might consider another system altogether rather than the autosiphon. It would take little to convert your system.

Drill a couple small dribble holes in the tubes just before they exit out the bottom of your beds.

Cut the tubes off at the height you want the water to reach in the beds. This setup may require something to hold the medium back to prevent the medium from being washed out the tubing and to prevent the roots from blocking the dribble holes.

Put a timer on your pump. Run the pump for 15 minutes very hour and a half (adjust as suits your plants, your climate). Once the pump shuts off the beds drain via the dribble holes.

This is the setup I have in the house cleaning my husband's guppy tank. It works flawlessly with no fuss, no auto siphon, no mess AND it saves on electricity because the pump doesn't run continuously. The plants are big and awesome. I'll snap some pics for you tomorrow.

Hi again ElfN.

I like the dripping standpipe idea you describe in principle, but the tiny weep hole does seem very "cloggable". Since building this setup I've heard that flood and drain isn't really necessary at all for a healthy aquaponic grow bed. I'm wondering of just a standpipe alone is sufficient.

What do you think of the idea of solid color tubing to inhibit algae from growing in the tubes? From what I read, algae need light (except for some recently created genetically modified marine algae).

Black tubing works fine. Algae can't grow without light so opaque tubing solves the problem.

You can't use a standpipe without a dribble hole. You'll end up with standing water and the growth won't do as well.

Here's a picture of the test setup of my flood and drain system and the proven setup used for cleaning the guppy tank. Nothing is fastened permanently. I have rubber bulkhead fittings which allow me to draw the tubing out of the fittings if I have to disassemble the system. These work well in the fairly thick wall of the pipe.

Flood and drain trial

Here are the things I learned.

The drain stand tube must be clear of all grow medium and exposed to light. This prevents the plants from overcoming the stand pipe and choking off the water flow. It also prevents the medium from washing out of one bed into the next and ultimately into your fish tank. I have a temporary dam installed at the stand tube end 2" short of the stand tube. This lets me visually check the dribble holes to ensure they stay free from blockage. If the water flow isn't correctly adjusted it will make surge/gurgle noises. This is only an issue if the noise bothers you. Adjusting the in-flow solves this problem.

The top of my stand pipe end is cut at an angle. I'm sure I had a reason for this but it doesn't instantly come to mind.

The grow medium MUST be ph neutral. Anything else cannot be moderated, causes plant damage, inhibits growth and causes damage to the fish. When you start up the system make SURE you check ph frequently. I use oyster shell to moderate the ph until it settles and if left in the system does no damage. I line the bottom of the plant bed with oyster shell before adding the plants and then the media. Oyster shell is not a universal fix. The ph of our water here is below five (rainwater). The oyster shell brings it up gently and naturally to 7.4. Ph greater than eight requires a completely different approach. I can't help you there.

Put a screen over the end of the feed tube coming from the pump to prevent medium from getting sucked into the tube and blocking the flow when the pump shuts off.

Supplement your feeding with liquid kelp. The fish alone cannot provide all the nutrient needed. Without the added nutrition I got white fly infestation. I got my best growth and fruit when I started adding kelp.

My inside guppy tank does not provide enough nutrient to produce fruit. My outside tank with a mess of goldies and the addition of kelp does just fine.

I know there's a ton of other stuff I should be telling you but it hasn't floated to the surface.

In rereading my post I need to note a clarification. My stand pipe dam is porous. It keeps the media back but allows the water through.

Also, if you want help making some working bell siphons, I can help you troubleshoot. Mine have been running consistently for 4 years and I've never had any issues after building them....

Thanks so much for all the advice. It's a lot to take in.

For now I'll be replacing the tubing with black to keep the algae out of that part of the system. I checked the tubing in the beds and it is clear so far, probably due to lack of light.

I'll definitely update at intervals or as things change significantly.