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.
I just had a similar problem with Jira HTTP <--> Apache HTTPS Reverse Proxy <--> Confluence HTTP where both Jira and Confluence base URLs relied on the reverse proxy and looked like https://myjira.myorg.com and https://myconfluence.myorg.com.
I also had regular proxy settings, and it turned out this was the culprit. Once I added -Dhttps.nonProxyHosts=*.myorg.com
to the JVM environment string everything worked sweet.
I had that problem before but in JIRA 4.4.1: https://answers.atlassian.com/questions/37569/jira-application-link-with-crucible-the-remote-application-is-not-able-to-connect-to
Check your base URL, check that you have an admin account on BOTH applications and check that the application name + password in Crucible match up to the one in USers -> JIRA user server.
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