I have no idea concerning the extent of your 11.5 project files, or how many places you have for this growing pain from the overly forgiving case insensitive aspect of IIS to the world of NW (and many app servers that enforce proper case). This is an application server constraint and not specific to MII (would be the same if you were on Apache instead of IIS).
It might be easier to fix the issues in your 11.5 codebase and re-migrate (you can always delete the project and migrate again). Leverage the IIS or NW logs to track down the errors, and perhaps searching for ".irpt", ".png", ".jpg", etc will help you find all of the locations where the file path is being constructed in your code or hyperlinks.
Look on the bright side, perhaps you will stumble upon some other areas to optimize and simplify your project code.