This really isn't a question. We struggled with updating to FishEye 3.4.7 plug-in for Jira. After the upgrade everything appeared fine, however once you start Jira the site will crash either intermittently or after a few seconds. I worked with Atlassian support and they suggested that I reset the Application Link with Fisheye which appeared to solve the crashes. But we still had random crashes. Here are the steps I used which so far appears most stable.
Steps to upgrading FishEye Plugin for Jira should include -
1) Remove Application Link to FishEye
2) Upgrade FishEye Plugin via UPM
3) Restart Jira Service
4) Create Application Link
5) Link Repositories\Projects (painful)
Hope to help others.