Regarding the special stage courses, I believe they are all real and all to scale. I just haven't been able to figure out exactly where everything is. Route 246 is easy because you can walk it. The other courses use the Shuto Expressway (the roads where there are the solid walls where you can't see anything and where the roads go through the curving tunnels are also the Shuto-ko) which pretty much negates any ability to walk the course.
The bridge, without question is NOT the Rainbow Bridge which goes out to Odaiba. I've been on that bridge many times and it is definitely not the bridge from GT3, however, the highway that runs from Hamamatsucho to Odaiba is called Number 11 which is very strange because I believe the real Route 11 track is out in Yokohama, about 20KM to the west. Last month I actually got a close-up view of the Yokohama Bay Bridge and it is DEFINITELY WITHOUT A DOUBT WHATSOEVER the bridge that is depicted in GT3. The ferris wheel has to be the one at the amusement park in Minato Mirai 21, which also happens to have a roller coaster. I'm not sure if the ferris wheel in Odaiba (near the Rainbow Bridge) has a roller coaster or not but the one in Yokohama Minato Mirai 21 definitely does.
If I had to make an educated guess, I would say that Route 11 is the area between Sakuragicho Station and the industrialized area out towards the entrance to the Yokohama Bay Bridge. Unfortunately, it's very difficult to get any concrete landmarks (such as are on Route 246) and much of Route 11 is not walkable and taxi fares are prohibitively expensive and would probably yield very little in terms of scouting the track.
I was staying at the top of the Landmark Tower during my last trip right there where it looks down right on all of this but the weather was very bad and we even had a typhoon blow through so the visibility was very bad. The only chance to see that side was when I was at the restaurant on the top floor as my room was on the opposite side of the tower.
I think on my next trick, I'll take a shot at scouting Route 11 a little more but transportation is a problem in that area since it's industrialized and there are no trains or public transportation convenient to the actual area where I believe the track is depicted.