I don't see why the process you describe requires root access... I think Net:FTP::Recursive is the perfect tool. If you have the access to do the remsh (I assume now you're on HP-UX) you should have the same access to the account you want owning the files on the remote system(s). As for changing the file permissions, that can be a simple script after you put the files out... using Net:SSH would be ideal. Avoid chmod -R though for obvious security reasons... I would instead build a list of files... maybe with the File::Find modules so you can chmod specific filenames/directories.

use File::Find;
sub process_file {
    push @files, $File::Find::name unless (-d);
    push @dirs, $File::Find::name if (-d)
}
find( \&process_file, "your src dir" );
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