I'm not sure if you've found your answer yet, so I suppose I'll reiterate what's been said in greater detail. You're missing one on the Death Mountain Trail and another on top of the Twins' House in the Kokiri Forest, right? All Gold Skulltulas in those areas only appear at night, so you first must make sure the sun has set. Chances are you've already done that, though, so I'll try and help where I can. I know the one on the Twins' House only appears when you visit as an adult; I'm not sure which Gold Skulltula you're referring to on the Death Mountain Trail, but chances are it's exclusive to Child Link or Adult Link.
My advice comes from the original Ocarina of Time, though. I haven't played the remake, so perhaps there is some sort of glitch. I would somewhat doubt it, though, as the developers tried to stay pretty true to the path of the original, right down to pre-existing glitches (none of which are known to erase Gold Skulltulas).
If all else fails and you just can't find the last two or you don't want to take the time, you could always take advantage of the glitch in a grotto near Hyrule Castle as a child, which allows you to gain infinite Gold Skulltula tokens and would bump your counter up to 100. That, of course, is up to you, and if it feels too illegitimate, it may be better to hold off on it.