hello asm, I've just built a neckthrough SG (I will be posting pics real soon) so I think I can answer your questions:
1. I think if you´re planning on using a maple top it would be a little more difficult because you have to be very accurate with the body/neck area, it has to fit perfectly around the neck. Mine is mahogany because I like it that way, but you can use the maple.
2. I also made a Les Paul copy, and I think that building the neckthrough was way easier than the set neck. To me it was easy to glue the wings and then planing the center piece to match the top level. In either case you need to draw your plans full size so you can check the angles and everything. And if you have experience in woodworking I would say go for it, build the three kinds of necks I would say the neckthrough was ther easiest, but please draw it first THEN cut, there´s one sayin: "measure twice, cut once"
3. I think you can use any kind of trussrod, I bought the Hot Rod trussrod from StewMac, it worked perfectly and besides in a neckthrough and a set neck and a bolt-on the trussrod works the same.
4. If you check this page www.everythingsg.com in the vintage area there are some ads where you can check the specs the SG´s have. I built a Standard so I use a 3 degree, but you can see a range from 2 to 4 degree, depending on the model. I think you wouldn´t have any problem if you use a 3 degree angle.
5. I use the Hiscock´s "make your own electric guitar", he shows how to make a setneck, a bolt-on and a neckthtough, I have learned a lot with that book, if you can buy it you would do yourself a big favor.
6. I use the guitarbuild.com plans, they seems to be very accurate but the scale in those plans are 25 1/2" and not the original 24 3/4" scale, take that in mind. In fact I use different pics to make it the more accurate as posible because I think the guitatvuild plans are a little too wide for my taste, check a lot of pics and you´ll be fine.
Hope this can help you, and I don´t think they´re stupid questions, you should see some of mine cheers
Alberto
(and sorry for my english, it´s not my native tongue)