Just use Dop Mii to install any missing IOS files you may need - no need to worry about updating system menu (unless you want to). I am still on 3.2 and have no problems
quicky looking at that guide it does not seem to mention a cIOS or anything like that - and you need one of them to play from USB - take a look at http://gbatemp.net/t207126-nus-auto-downloader-for-windows
My apologies - as you are on 3.3 you do need to update in order to run start patch or priiloader to prevent disc updates as there are no hacks for that version of system menu. Follow the sticky guide to update your wii to 4.2 and then install priiloader or startpatch to block disc updates.
games do not require a specific version of system menu - just use a WAD Manager and install the IOS you need. Install priiloader and tell it to skip disc updates. I am on 3.2 and not found a game i cant run yet.
none of that should cause a brick and the chances are pretty slim - but possible - say you have a power cut ? thats the only main danger i can forsee, and I have installed bootmii as a boot2 on both my wiis and no bricks