CloudBees Support Engineer here! We offer a free Assisted Update service to customers for exactly this reason. We will examine your existing Jenkins installation, compare it with the target version you would be updating to, and outline any possible snags that you would need to address during the process. We also help ensure that you have a good backup so that you can roll back if need be, and if you are a Platinum customer a Support Engineer will hang out on a conference call while you perform the update. We've done loads of successful updates with customers this way, I think it's one of the most useful services we offer. Updates don't have to be as painful as you've described!

Jenkins has used Jira for bug tracking since before GitHub existed, so although the project's code and all plugins are now managed on GH, bug tracking continues to live in Jira. Anyone can create an account and add issues here: https://issues.jenkins-ci.org/secure/Dashboard.jspa All plugins track issues there, so you just put the appropriate plugin, or "core" for Jenkins itself, in the 'component' field and the issue should be assigned to the right person.