Hmmmm. Well aside from doing a system wipe on the WiiU I'd personally just update to 5.5.1. We've been waiting a while for IOSU and it's only speculation right now on what firmwares will be supported. Don't take my word as gospel but I'd update it. If/when the IOSU exploit comes out I won't have troubles finding a lower firmware WiiU online. Might as well enjoy full hassle free homebrew right now.
I'm tempted to update it, but knowing my luck it would still not work somehow. Honestly though, from what I've seen, the current setup (which works on 5.5.1 too) can do basically everything (homebrew, backups, etc) except for play games online, which I don't care much about.

