Now I have checked/deleted/added the Handler Mappings, ISAPI Filters, and ISAPI and CGI Restrictions until I am half-mad. I have deleted the connector with wsconfig loads of times, and the only thing I see that stands out is in the isapi_redirect.log:
[debug] handle_notify_event::jk_isapi_plugin.c (2505): [/] is not a servlet url
I have checked permissions, checked everything I can find, and this time the forum below is not the answer. The IIS server serves up all the cfm files, etc. fine, it is just using the dir only that we have a problem (again).