Sorry to create a new post but I guess when them moved the forums you can't reply to posts made prior to the move.
Downtown,
The Great Lakes should be showing up, I remember playing with that during my testing work. Let me double check it, can you give me the parameters you are using (lat/long/degrees).
Detail on very small areas will always be a "hit or miss" proposition. The AH terrain data set has a resolution of 0.5 miles, so small, significant areas (like Ford island) can be missed. You'll have to add them in yourself using the AH editor).
Regarding your terrain spanning two tiles... simply download all the tiles you want and run MapMaker as you would normally. MapMaker will seam the tiles together. You don't have to do anything else other than the download. This way you only have to download the tiles you want to use as you need them, rather than being forced to get all of them at once (including ones you'll probably never need).
CBI should work, I remember looking at the Hump during testing.
-Ogre