If I understand correctly there are two options. If not, please further explain the issue.
(1) You have text endpoints files from trajectories you created on the web. Rename these to a name such as tdumpYYMMDDHH, where YY is the 2-digit year (12 for the year 2012), MM the 2-digit month, DD the 2-digit date, and HH the 2-digit start time of the trajectory. Put these files in a directory such as c:\hysplit4\cluster\endpts, then run the cluster program. See the example trajectories in c:\hysplit4/cluster/example/endpts.
(2) There is meteorological archived data at http://www.ready.noaa.gov/archives.php
you can download to your PC, then run the trajectories.