I am trying to configure an Application Link from my JIRA (version 5.0) instance to my Crucible (Version 2.6.1) instance and I get the error The Remote application is not able to connect to 'Meredith Corporation JIRA'(JIRA) by using the URL 'https://XXXX.XXXXXX.XXX/dt'.
These instances are on separate servers and I've confirmed connectivity between the servers in both directions (https on port 443) using the SSLPoke class I found referenced on your site.
Both of these instances are behind their own Apache server and both are running SSL.
There is nothing in either the JIRA or Crucible logs when this error occurs.