1) I put an air pump in the line after the pump, as I am going to be aireating now that way instead of an air stone - found this makes it take longer to fill the flood tray.

2) If I flood the tray to only about 1/2 the height of the overflow, I find that the balls do not seem to float as much because of the weight of the other balls on the top. Is this the solution?

Long as your plant roots get down into the media being flooded... Is the tray covered with a lid and holes for the plants? This would probably keep the media in place as well as keep algae from forming on the media surface and cut down on evaporation.

So you're only aerating the water being pumped into the media chamber during the flood stage? Aren't you using the organic nutrients? I would keep an airstone in the nutrient reservoir. No need to aerate flood water if the nutrient reservoir is constantly aerated. If you don't aerate reservoir won't it go anaerobic?

The hydroton will normally sink, usually its only a few that stubbornly keep floating after an hour or so.
You need to flood it about 1"-1.5" below the top of the hydroton as it will wick moisture to the top.. keeping it moist.
If you flood above the hydroton, the evaporation rate will increase by a large amount and you will wet the stems which may cause them to rot.

Good luck with the toms

I did find out that after a few waterings the balls didn't seem to be as floatacious as they had been - quite a relief. I think they just float a lot when they are brand new / very dry.

Here is what I have now:

- 5 gallon bucket as the res. - I find it takes only 2 gallons to completely flood to the overflow level, and as was said, I am only flooding to about half of that height b/c the rest will wick and stay moist. So it's probably only about 1 gallon to flood the tray. This is great! Saving $$$ on nutes in my small system with an efficient reservoir and flood tray.

- I put the air stone back in the res. after charlie little's comment. I was afraid to because I don't have a lid for the bucket (yet!) and a little bit of water drops tend to jump out of the bucket. I put some black/white poly on top of the bucket as a temporary lid and it's working fine to keep the water droplets inside.

- I am considering drilling a hole very near the top of the bucket and attaching a fitting so that I can easily make a light-tight reservoir by routing the hoses through there. The power cord for the pump would be a challenge though, unless I can get an air lift to work, then there would be no bulky end to a power cord so it would be easy to set up.

- I put black/white poly in between the plants so that you can't even see any of the clay balls. I think I need to set the timer down to maybe every five hours instead of 3 as I think there will be ample moisture in there.

- Tomato seedling leaves are curling really bad and I think it may be because they are too wet so I didn't irrigate at all today and will cut the timer back more for tomorrow when I go into the office.

- Once the seedlings take off a little more I will try to post some pics.

- I am not using organics yet but want to try at some point in the future.

I took some pictures - can't resist sharing :)
Here are the tomato plants in the system:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129812156255746

Curling tomato leaves:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129829336124946

Bucket reservoir:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129855105928738

Inside the bucket:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129880875732530

Bottom of the tray:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129906645536322

Temp/humidity:
http://picasaweb.google.com/richard.eric.crawford/Hydro1/photo?authkey=jXCsFSXkTn4#5171129923825405522

Here is the entire album that has pictures at two weeks of my lettuce crop. The lettuce turned out to be delicious. The purple basil was too strong for my taste but others seem to like it. I think I am a sweet basil person.
http://picasaweb.google.com/richard.eric.crawford/Hydro1?authkey=jXCsFSXkTn4