just place these files into the /pb folder on your server.
execute the cmd /rcon pb_sv_restart on your server
check if it worked out with /rcon pb_sv_LogPort
now u should see the following line into your console:

^3PunkBuster Server: pb_sv_LogPort = 11003 (1 to 65535)

if your server tells u any different shit then u still have 2 more options.

enable "show hidden files" in your FTP program 
find the ./callofduty2 folder (marked as hidden folder)
and upload the 3 cfg`s in there.

/rcon pb_sv_restart
and the check again...
/rcon pb_sv_LogPort

ok if it still dont work u can use our rconscript. so u can load the settings through rcon