I now have it working with UCM clearcase.
I wrote a ratperl script (JiraMakeAct.pl) which will give the ClaerCase user a list of their assigned JIRA tickets for the stream they are working on and it will create the activity with the proper name/header/title for FishEye. This is very handy for developers. I also wrote a hook to prevent the use of standard mkact (other than rebase/deliver) to make sure they use JiraMakeAct.pl
Overall, it works reasonable well as a replacement for CC/CQ integration. And even though the intra-branch diffs are a bit hard to set up, they still have ClearCase for that. But all the source shows up in JIRA which was the goal.
We plan to migrate from ClearCase next, so its only an interum solution. If anyone thinks they can use these pieces, let me know and I can post them somewhere.
I don't have a configuration to share with you, but you can check out the official Atlassian documentation about how to setup Fisheye with Clearcase. However, please be aware that on April 4th 2012, Atlassian is ending FishEye support for IBM ClearCase. For more information on this decision please see End of Support Announcement for IBM ClearCase