My galaxy nexus is of yakjuxw variant. Will it not destroy my phone if I change it to takju or yakju version? I'm just aware that doing so will delete user files/settings.
I did not have any issue making a similar change myself, using the guides online that walk you through switching your Samsung or Telco branded Galaxy Nexus (on the Samsung upgrade track) to a Google branded one on the much faster Google upgrade track.
Don't skip any steps, and be sure to back everything up, and be aware that you are probably voiding your warranty. I linked to a 4.1.1 upgrade guide; I am sure there are newer ones out, though most of the guide will be identical.