If you are stuck on the Lionel model I wouldn't think twice about taking Bob's brother or anyone capable up on the $100 plus a little per axle. A layout as big as your layout will cost many thousands of dollars. Dropping another grand or two to fulfill your dream probably isn't going to make a big difference in life.
Personally the 3rd Rail model would be my route since I'm not hung up on the Lionel gizmos and I could install what I want to suit my needs.
For the MTH engines, there are most likely equal or better out there in 2 rail and install the electronics to suit.