I don't have OOT 3D but I did this quest alot on the N64. It is possible to get the Biggerons sword before you face Bongo Bongo. Its really east to defeat with it. For Ganondorf I usually used the Master sword to deflect the energy balls then when it is stunned I switch the the biggerons sword. You get less hits but the they tend to be stronger. My first few runs through the game I used the Master sword. I didn't really know about the Biggeron's sword till maybe 5 times through the game.
Few things I would change in the video mainly has to do with Epona's direction it is facing when going to another area. When you get back to Epona you can just hop on and go without changing the direction and wasting a few seconds. Other then that good video.