The issues with Waninkoko's updater is that it foolishly trucha signs ALL of your IOSes. That is not only unneeded, but it has some very bad side effects. Team Twiizers coded a little "joke" into the latest Homebrew Channel in which if you have the IOS that runs the HBC trucha signed, the HBC displays upside down! Also, if the hackmii installer cannot find a "sane" IOS, the installer won't work. Both of these problems arose after people updated with Waninkoko's updater (which I am still not sure is official, since it has never been posted in his blog)
Anyway, I started with an offline installer as soon as I found out what IOSes were updated with v4.2. Nintendo now stubs 222, 223, 249 and 250. They also remove the "HAXX" id as well as the "DVDX" id. The old bannerbomb was blocked and boot2 is overwritten by boot2v4 (overwriting your bootmii if your boot2 is a lesser version).
So, my updater does not install the stubs and does not touch boot2. It updates pure IOSes of the latest version, as well as new shopping channel. The system menu still blocks the "HAXX" id of the old HBC, which is why you must update your HBC before performing this update (v1.06). There is also a new v2 of bannerbomb that works with v4.2. It works great
