To expound on what ferday is saying:
A. On windows the total path length, including the file name *and* the directory names, must be 260 characters or less. The filename itself must be 255 characters or less. Under OS X, file names are also limited to 255 characters. But, the big difference is, the path name, including the directory names, can be much longer. It can be something a little greater than 1000 characters total. I just tested with 1000 characters and it worked. Something like 1020 did not work. So a much bigger overall limit.
You can fix your files to work on windows too, by changing DIRECTORY NAMES to make them smaller. In particular, if you have files deeply embedded in multiple directories, you can reduce the names of these directories, or just eliminate any that are redundant. Like "Music/FLAC/Classical". That could just be "Music". As an example.
B. Once you have files imported into MC, you can use the Rename, Move, and Copy tool to change file and/or directory names in a programmatic fashion. Ferday has linked you to the wiki article on the tool, should you decide it's something you want to use.
Brian.