Yes it's easy to do. You do not need waninkoko's updaters. Firstly you need to make sure that you have all the needed IOS's installed. you can download and install them from wads. The wads can be made with the NUSD downloader. You could also download and install the CIOSCORP v3.3 set. It has all the needed IOS's so that should do the trick if your not sure what you need. It will also let you play backups from the disk channel.
Secondly you need to install all the missing IOS files that you downloaded. Thirdly download the latest system menu version for your region and install that wad. That will put you on 4.1. I would actually just recomend the cIOSCORP 3.3 install to get you where you need to be. It will ensure that all the system IOS's are in place and trucha friendly as well as bypassing the need to do any further IOS patching ect to make any backups and such working. It makes quick work of the task of manually updating.