Look at section 13.6.4. That's at least the section in the 5.0.0-alpha manual.
Most full-text variables described in the following items must be set at server startup time. For these variables, a server restart is required to change them and you cannot modify them dynamically while the server is running. If you modify full-text variables that affect indexing (ft_min_word_len, ft_max_word_len, or ft_stopword_file), you must rebuild your FULLTEXT indexes after making the changes and restarting the server. To rebuild the indexes in this case, its sufficent to do a QUICK repair operation: /.../
And, here is what the manual says about the magic number 4:
The minimum and maximum length of words to be indexed is defined by the ft_min_ word_len and ft_max_word_len system variables (available as of MySQL 4.0.0). See Section 5.2.3 [Server system variables], page 238. The default minimum value is four /.../