IMO remove all the silicone as you can not guarantee that the new silicone will ad hear to the old stuff properly.
3M has some new silicone it is clear and is marine grade says that it is safe for aquariums so the next one I do will have this silicone. The yellow is from the skin that forms on the silicone reacting with waist in the water. What I normally do is silicone Waite 48 hours put water in tank and let sit for a day and then empty it there will be a slimy skin on the silicone and if you remove the skin there should be no yellowing. If you can get black silicone I would use that and any discoloring you would not be able to see.
You can get a corner tool from Home Depot it is a red plastic tool with a white rubber rounded blade. also use masking tape in the vertical corners this will give it a nice clean look apply the silicone then remove the tape do the bottom to side corners right after you remove the tape that way all surfaces bond as one piece and while you are at it if you have a black trim you can re silicone that also. I just run a putty knife along the outside edge and then lift off the black trim, you just have to be carefully to not break the plastic. When lifting the trim off move your hands down so where the trim and top edge of the tank meets is not to far apart this helps keep the trim from breaking.

Bill