What about covering the logo with a rectangle of packing tape, then using a sharp blade/razor, like an x-acto(r), and carefully cut around the letters removing the extra tape, leaving the letters covered. then, painting and once dry removing the tape, thus revealing the original lettering.
Another route could be to just paint over it then stencil it back on, in which case you may consider redoing the writing with an alternate font or something to go along with the zelda theme. Either way you do it i foresee the (R) and TM
being a pain to get on there.
Or you could hand letter it back on if you're good at calligraphy.
It sounds like it will look real sweet when you are done. You should def post a finished product pic.