For something like that I would retain a good architect who has ties to a good structural engineer. Savings in day to day cleaning effort and long term maintenance costs would probably pay for the up front professional services over time. Even if you're an architect or engineer, having another set of eyes look at it would probably pay off.

Based on my experiences with my own I'll try and answer some of your questions.

First of all it is critical to decide how you want to use the space and what you intend to grow. That will dictate how it has to be built. Based on your description, you will need more glass area to grow anything year round. Think about how the sun moves through the seasons as far as angles. Low in the sky in winter and high in summer. Having the glass true south is a must, that is a mistake I made, and now I have to supplement the sun to get enough direct light for some of my plants different times of year. You can grow tropical plants without heating the space if done correctly. I grow citrus in mine and it is a passive greenhouse in zone 5 outside Denver, CO. As far as material I personally would stick to mold resistant woods and stay away from metal completely. Humidity is a real issue in the colder months, especially if you want a tropical feel. My interior is sealed cedar with no problems thus far. There is however some issues with the sealed steel holding retaining walls. As for company's, books, advise, etc., there wasn't much out there when I was researching. Although my greenhouse is not what you are talking about building, I will attach a photo to give you some idea of some of the remarks. This is 16x32, 28' tall at crest. It has a 8x32 heat sink at 8 feet.

Thanks for the input. Basically, it would be a glorified window sill. I'd use it mostly to overwinter tropical potted plants (so I'll need some type of lift with ropes or something) and maybe grow some edible greens during the winter months. Also, an early start for tomatoes and peppers. In summer it would be mostly free of plants.

I'll need to think about watering and drainage. If it's a windowsill 40 feet long, odds are at least one of the planter saucers would spring a leak.

Lazy, this idea looks interesting. Now I may have to rethink my original idea. The reason I wanted my little indoor greenhouse area above the first floor is that the building site is on the north slope of a hill, so the south end of the house will be partially below ground.

I agree with Lazy with respect to making it easier and probably less costly taking the approach he did. With the difference in zones and lower temp.s in the winter months you may have to give humidity control some extra thought. As I mentioned in my previous post It will depend on how you want to build it. Dirt floor, partial finished, or container plants? I do think the heat sink is important to help stabilize temp.s year round without high HVAC impacts. 8 feet is a real key, and should be real simple with the house being built into the side of the slope. For example, I have a dirt floor and when the outside temp. drops below 55 degrees the inside humidity starts climbing at night, as well as cloudy days, It will often go as high as 90 percent if I watered that day or sprayed. One difference is I don't incorporate the temp.s with the inside of the house as Lazy does. I have a friend with a greenhouse very similar to mine and he leaves his open almost all the time and uses the humidity in his house and it works out great. Rock based mulch will control mold and fungus in soil, it took me quite some time to get that figured out! I would also stress air movement of some type in the area.

This leads me to another question: which option would be more energy efficient: a 1st floor greenhouse area with very tall windows that start at about ground level, or a clerestory area greenhouse (just above the first floor) with much shorter windows?

If it were me I would try a combination. First floor level without windows, second floor level with windows and roof with operable skylights for ventilation in the summer. As Lazy indicated the roof will act as shade in the summer so if you are growing citrus for example, they need direct light. When I say first floor without windows I am referring to foundation on three sides, cut into the hillside. That will act as a heat sink to help moderate temperatures. This combination, I believe, would be the most energy efficient. I have attached a drawing to help visualization.