Scrum is only a start point for your process, look at it, keep the bits you like, ditch the bits you don't. It is NOT a religion, (despite many people's insistence on adhering to its holy scriptures).
So, bearing in mind this, the point of Agile as a whole is to remove impediments (like management processes) to enable you to perform your work as easily as possible, however, it realizes that without any management process you may go 'off track', so it introduces a few different processes designed to help you keep yourself organised and working in the fright direction. The main processes that do this is regular updates and team communication.
So this means your epic is "do some work" but you can't realistically do all in one long go without involving a lot of risk (ie when you finished you'll show it, and only then will you know if you did it correctly). So, you break that epic task into smaller pieces that you can show to others to prove that you're still working on the right thing, and that it still fits the desired result.
It can be difficult to understand how to split an epic of 'do an upgrade' into smaller, bit-sized pieces, but I think if you started work you'd quickly be splitting it up anyway. The problem is one of perception, a mental block that stops you thinking about it (like seeing a blank page and not being able to start writing). You can imagine yourself performing the upgrade, and you'll naturally split the tasks up - write them down and you're pretty much done splitting the epic into stories. For example, to do such an upgrade you might have sub-tasks such as provide a new environment, upgrade to latest JBoss, upgrade the DB, document the configuration, test the system, upgrade the code (which in turn gets turned into upgrade each component or layer depending on your system).
Personally I think 2 week sprints are duff, I worked best with 6 week sprints once upon a time, so do not be afraid to change the timing, but do not increase the sprint times to remove the value of them - you need to show progress after each one, or its pointless having sprints at all. And if you don't show progress, there's no point doing Agile. So keep it to reasonable times and release often. If that means pulling a double-sprint now and then, so what - do it. (many people will say "but this will affect your velocity", and I say "sod velocity, its about real progress not management reporting").