Is it the indexing giving you the error or trying to access the topics that are? You should be able to view the topics themselves, but if you click on forumdisplay.cgi or Ultimate.cgi you'll get a 500 ISE if the permissions on the files aren't correct or your server isn't setup to run cgi/perl correctly.
I'd reset all permissions on those threads files to 777 and re-try the indexing. A test script came with the old ubb to check permissions on the folders and files - check yours to see the results. I believe it was kept in the same folder as the re-direct scripts
