Take an old tire tube and cut in half lenghtwise and wrap it around the downtube and top tube. It will cover up all of the Fuji logos. I don't think they can be removed because they are under the clear coat. Before you do the downtube, remove the bottle cage bolts and cover holes with electrical tape before you wrap the downtube with the tube. This will help keep any h2o out of your frame. I did this with mine and it helps to give a cleaner look. I also don't use water bottles so removing the bolts was not a big deal. I have found using the tube around the frame also helps protect it from lock rash.
Get a solid black saddle, all black tires, black or blue bar tape. I just think you got too many colors and logos going on with it.