This script will let you save out a text file with the current MRU list. You can also import one of these saved files and restart AE to set the custom paths.
http://www.leapfrog-productions.com/Scr ... U_v1_1.jsx
To use it you must edit one line in the script, it should be line 23 and read as:
var textprefs = new File("C:\\Documents and Settings\\YOURLOGINNAME\\Application Data\\Adobe\\After Effects\\Prefs\\Adobe After Effects 6.5 Prefs.txt");
This line must be edited to reflect the location of your text prefs file. Usually the only change needed should be to replace the YOURLOGINNAME text with your user login name on Windows machines.
And, please backup your prefs file before using this script

This script has only been tested on windows so if there are any issues on the mac side please post.