I built a similar 12x12 greenhouse from 2x4 treated lumber, but I painted after framing before glazing. Don't forget to use a good oil-based primer coat before painting. I have been through 2 years including 60 mph winds, 8" of snow, and 100+ F summer temps satisfactorily.

I have some suggestions for you to consider. First, most GH owners would recommend twin-wall polycarbonate glazing. Second, you can stiffen and insulate the greenhouse by covering north wall with 1/2" treated plywood with 2" foam insulation panels. They come in 2'x8' panels which fit nicely if you space your 2x4s properly. You can do the same (with smaller benefit) by enclosing the bottom 2-3' of the side walls (as kneewalls). Little useful sunlight enters here. Third, with these changes, you don't need diagonal braces. Nor do you need cross braces on the rafters if the 12' peak length is not exceeded. I recommend using galvanized nail-on straps (not sure what they're called) at the peak and other ends of the rafters to hold the joints together. With primer and 2 coats of exterior paint, these have held up well so far.

Now for condensation, venting, etc.... you will need good internal circulation fans to reduce mold/fungus problems. I think you will want the roof-glazing to overhang the sides by ~1' to keep rain out. Also, I think you will want to attach the glazing panels to the exterior of the studs/rafters and cover the joints with aluminum T-bars. Then, seal the seams with silicone. I suggest you look at the construction details at http://www.cloudtops.com/polycarbonate_verolite.htm. You will also have to provide some means of maintaining high enough humidity when you heat in winter: misters, foggers, etc.

If you plan to keep any plants in the GH during summer, you will need shadecloth, misters/foggers for cooling, and larger exhaust fan.

Other thoughts on your specific questions: By windows I think you mean roof vents. This will be needed for summer use. See how on-line GH vendors do it, especially the automatic open/close devices. I built mine from 1x2s but I have trouble sealing from rain. The glass/aluminum door is fine. Check your local building code or hire a licensed electrician to do the electricity business safely/legally.

I will gladly answer questions and will welcome comments by others correcting or improving upon my comments.

I had considered buying an aluminum/polycarbonate cold frame and just using the top for the roof vent. Probably a good choice.

Thanks for the feedback. I'll look into a supply of twin-wall poly panels. If the cost is too high compared to clear single pane poly corrugated panels, I may not upgrade. Bear in mind, I get snow once every 5-10 years. My propane heater is up to the task despite drafts. I've even had PVC hoop greenhouses which were covered in 6-mil poly sheeting that kept everything nicely above 50-degrees with 30-degree winter nights.

As for the plywood, can I do that with just 3 feet all around and forgo the diagonal bracing? My yard runs East/West and the GH will be on the south line of the property. Thus, the north side of the GH will have maximum visibility to the yard. I want to minimize ugly.

Framing: I've looked at the framing hangers at Lowes. They have some very good ones for hanging the rafters; connecting them to the peak ridge of the roof and the top rail of the side walls. Some actually have the word "Hurricane" in their description. I'll use similar connectors at the base of the walls.

As for ventilation, I used a calculator at:
http://www.littlegreenhouse.com/fan-calc.shtml
to determine the fan size. Their 16" fan should handle that volume of air. However, I'm wondering if I'd only be running the fan at maximum capacity to do this. If that's so, then I should move up to a 20" fan so that the motor will only be working in the middle of it's range.

I've saved the four roof vent panels from the HFGH that I had last winter. I'm going to see if I can't rig something to make it fit the design and be waterproof too. ACF Greenhouses has temperature triggered automatic openers.

Electric: There is a storage shed within 10 feet of the greenhouse site with electric outlets. If I tie into the shed's power supply, what exists in the world of GFI circuitry for doing so? I've added outlets within the house by just daisy-chaining from one outlet to the next. I know that is WRONG for connecting an exterior curcuit (the GH) to an interior circuit (the shed). I imagine it's a similar daisy chain, but the greenhouse goes to a GFI device contained within the shed's interior which is hooked into the shed's power.

Here is a link that might be useful: ACF Greenhouse Fan calculator

Check out the framing of these commercial kits (see link below). I used these as the basis to convince the county building inspector to approve my design.

I can't guess whether the poly panels you use will provide as much stiffening of the frame as the polycarbonate twin-wall panels. If so, kneewalls on 4 sides is ok.

I have no comment on the safety of outdoor electrical designs except follow the code or hire a licensed electrician.

Here is a link that might be useful: CedarBuiltGreenhouse