Hello Steve
1. If you made your system out of clear plastic it would look like something out of a Swamp Thing movie and smell like one too.
Disney I'm sure washes off the slime before the public sees them.
But if you still want to build one you can buy clear PVC at
Aquatic Eco-Systems, Inc..
2. Short plants like lettuce seems to be a favorite plant for NFT. Tall plants like tomatoes and cucumbers usually use some type of medium.
3. The more light you can keep from hitting the water the less algae you will have. Algae isn't necessarily harmful to plants unless it gets so bad that it starts to clog the medium from getting oxygen to plants underneath.
Ron