Unlike in the original OoT, in Master Quest, you can skip getting Ruto altogether. To do this, you will have to go the back way to the boomerang by skipping the water jets. In order to skip the first water jet, get ISG, roll into the jet, and open the door. Because you have ISG activated, the water jet will not be able to push you away. Note that you also don't have to get ISG off of the chest if you have bombs. Now for the second water jet, simply angle yourself with its right side and backwalk into it to get lifted over to the boomerang.
Do a jumpslash, and then crouch stab the right side of the Song of Time block to kill the gold skulltula. Now walk over to the left edge of the block, and through the boomerang at the wall. If you don't move, the boomerang should go through the wall, and then loop around and grab the skulltula token. In a 100%, this trick allows you to visit Jabu-Jabu's Belly only once.
Get up against the door and align yourself in the center. Turn around and take 3 small steps and then aim your slingshot at the cow switch. Shoot a deku seed, and quickly exit out of the slingshot camera and turn around to open the door. If you timed it correctly, the door's opening animation will be interrupted by the switch cutscene. This will cause the room you were going into to load, and some of the features in the other room to become unloaded. Now you can jump onto the rising platform and use a megaflip off of either a bomb of a chu to get to the door.
Note: Sometimes if you do not move a little away from the door before opening it, you can walk too far through it while preforming the actor glitch and get stuck. Taking the 3 steps before shooting the switch should overcome this possibility, but just in case, you can do a backflip right after preforming the actor glitch.
For this method you will need a bottled fairy. Use a megaflip to get over to the red slimy thing and run into it with low health so that you die. Wait for the fairy to heal you and you will have temporary damage invincibility against the red slimy thing (meaning that for that brief time you can't take damage). Now quickly walk by it and open the door.