Nikhil,
You perhaps have not gone through the recommended pre-migrations checks. It has been clearly mentioned to maintain proper case before you start migrating the stuff.
The best way is to create a copy of your IIS working folder and then replace the paths using some text editors or file search tools. Notpad++ worked best for me to search all files in a folder containing some path and replace it. Then you can migrate it from the copy to NW based MII server.
This way both 11.5(as you made changes to copy) and new version would be working at the same time and you get a chance to cross verify stuffs and functionalities.
Hope it helps.
Best Regards,
Swaroop