Pruning the roots usually dosen't hurt the plants depending on how much you prune. But pruning too much can do real damage to both fruit and foliage. After all the plants rely on the roots for not only the mineral elements (
nutrients) they need for photosynthesis, and that converts the nutrients into all the compounds the plants need to grow (especially the sugars the plant uses for the fruit). But they also rely on the root system to be able to drink the water they need. If they cant drink up enough water to replace what is transpired out through all of the plant foliage, they will just wilt over and become week.
kiwi2
I get why ""Kiwi"" now. Anyhow if you built your system like in the link, it will look nice. 2.5 gallons would be a good size for growing plants like peppers. You certainly can try growing tomato's in it, and see what you think. For me, I grew some in a flood and drain system using 2 gallon buckets, and I personally wont be using that small of a container for tomato's in the future.
P.S.
Not to be pessimistic, but the system I built for the tomato's using 2 gallon buckets on top of PVC tubing became top heavy. So I had to use bricks to set the buckets on or it was going to break. I don't really know how strong yours is, but if it was anything like mine, you'll want to be aware of how much weight those buckets are holding, and how easy they'll tip side to side. Here is a link to the thread of the tomato plants I grew. Notice how I have the weight of the buckets supported using the bricks.
http://www.hydroponicsonline.com/for...y-tomatos.html