In your script, insert something like -
system ("chmod 755 cgi-bin/yabb2");
system ("chmod 755 cgi-bin/yabb2/AdminIndex.pl");
system ("chmod 755 cgi-bin/yabb2/FixFile.pl");
system ("chmod 666 cgi-bin/yabb2/Paths.pl");
system ("chmod 755 cgi-bin/yabb2/Setup.pl");
system ("chmod 755 cgi-bin/yabb2/YaBB.pl");
system ("chmod 777 cgi-bin/yabb2/Admin");
system ("chmod 666 cgi-bin/yabb2/Admin/*");
system ("chmod 777 cgi-bin/yabb2/Boards");
system ("chmod 666 cgi-bin/yabb2/Boards/*");
system ("chmod 777 cgi-bin/yabb2/Convert");
system ("chmod 777 cgi-bin/yabb2/Convert/Boards");
system ("chmod 777 cgi-bin/yabb2/Convert/Members");
system ("chmod 777 cgi-bin/yabb2/Convert/Messages");
system ("chmod 777 cgi-bin/yabb2/Convert/Variables");
system ("chmod 777 cgi-bin/yabb2/Help/English/Admin");
system ("chmod 777 cgi-bin/yabb2/Help/English/Admin/*");
system ("chmod 777 cgi-bin/yabb2/Help/English/Gmod");
system ("chmod 777 cgi-bin/yabb2/Help/English/Gmod/*");
system ("chmod 777 cgi-bin/yabb2/Help/English/Moderator");
system ("chmod 777 cgi-bin/yabb2/Help/English/Moderator/*");
system ("chmod 777 cgi-bin/yabb2/Help/English/User");
system ("chmod 777 cgi-bin/yabb2/Help/English/User/*");
system ("chmod 777 cgi-bin/yabb2/Languages/English");
system ("chmod 666 cgi-bin/yabb2/Languages/English/agreement.txt");
system ("chmod 666 cgi-bin/yabb2/Languages/English/censor.txt");
system ("chmod 777 cgi-bin/yabb2/Languages/English/*");
system ("chmod 777 cgi-bin/yabb2/Members");
system ("chmod 666 cgi-bin/yabb2/Members/*");
system ("chmod 777 cgi-bin/yabb2/Messages");
system ("chmod 666 cgi-bin/yabb2/Messages/*");
system ("chmod 777 cgi-bin/yabb2/Modules/Digest");
system ("chmod 777 cgi-bin/yabb2/Modules/Digest/HMAC_MD5.pm");
system ("chmod 777 cgi-bin/yabb2/Modules/Digest/MD5.pm");
system ("chmod 777 cgi-bin/yabb2/Modules/Time");
system ("chmod 777 cgi-bin/yabb2/Modules/Time/HiRes.pm");
system ("chmod 777 cgi-bin/yabb2/Modules/Upload");
system ("chmod 777 cgi-bin/yabb2/Modules/Upload/CGI.pm");
system ("chmod 777 cgi-bin/yabb2/Modules/Upload/CGI");
system ("chmod 777 cgi-bin/yabb2/Modules/Upload/CGI/Util.pm");
system ("chmod 766 cgi-bin/yabb2/Sources");
system ("chmod 755 cgi-bin/yabb2/Sources/*");
system ("chmod 766 cgi-bin/yabb2/Templates");
system ("chmod 766 cgi-bin/yabb2/Templates/default");
system ("chmod 666 cgi-bin/yabb2/Templates/default/*");
system ("chmod 766 cgi-bin/yabb2/Variables");
system ("chmod 666 cgi-bin/yabb2/Variables/*");