I know what you mean, corey. Thanks to the Obama administration, this thing got a big boost and has been expedited quite a bit. The franklin arterial project is following a similar path, because phase II will include engineering and feasibility studies, all of which will take place BEFORE funding is in place, so that WHEN funding is in place, it will be just a matter of saying "go". Franklin, Cumberland, and several other City streets are actually state owned highways, which qualify for additional funding. So that should be useful, assuming the foresight of local and state planners and politicians ever aligns...
As for the route, I have no idea. I know that the last connection between Portland, Freeport, and Brunswick was about 50 years ago, with the Maine Central Railroad, which I believe utilized a route that skirted the peninsula (i.e. it did NOT go through bayside or the waterfront). I think that's probably where this line will be, too, (outside of the peninsula) but I have no idea where. At one point a connection that would have required a rail bridge over forest ave was contemplated, but was rejected early on due to the high cost.
I also know that the regional director of Amtrak has expressed willingness to discuss a passenger platform somewhere on the western waterfront, by Gorham's corner, but that is just an idea at this point. Also, I don't know if service would just halt there, or continue northward. It would make more sense to continue northward along commercial, but as I said I really have no idea where the planned extension line is.
I'm pretty excited about this. Linking cities together by rail is an excellent idea. Not just Portland to Boston, but even Portland to Freeport would be great. Freeport is a walkable tourist shopping destination (in fact, its the biggest draw in the state) and a rail stop there will be perfect, whereas a rail stop in Kittery would hardly be of benefit to anyone. Did I mention freeport is awesome? What a fun little town. Granted its a tourtist destination and not much else, but still fun all the same. The movie theatre will be great.