I'd probably opt for following the book, with the modifications mentioned. I'm not a stickler for absolutely following the book. For starters how is a 2D paper map to be projected onto a sphere while preserving distances given in the book? Given it's The RedBook of WestMarch, how reliable are Bilbo's measurements, etc, etc, etc.
... a project form a book, where people measure everything whyte laser-range finders and include overall topography in book included digital form.
Making corrections from the book in terms of global geogaphy would not be such bad thing. Re-thinking city-building may have some extreme situation issues, doe, i dont think any book ewer described a town to the last detail of all its buildings (also, untold history parts of those cities may be used to give it a reason -- Nero ruined a whole city and other build monuments around a damn tree in our past too
) - there is a place to fit some of the needed stuff there. Also, its middle earth - some structures hold or deform solely by their own will - its a damn wizzard and demon world !
Who knows what tampering did the race of the moria-demon do to Earths liqid core for geologic anomalies in a global level in all the ages ...
Doe, i really would be impressed, if in later stages, the AI life of ME would be whyte some middle-age everyday life thinking. There is newer enough complexity and gives s more "alive" feeling of a lpace, than just statistics based chaotic/sporadic population movement implementation ... (that complexity means - yes, witchcraft does headache to science people, but must be complex enough, to convince them, that its based on tampering whyte quantum physics and chaos theory
)