This version (unlike the original) requires you to get all of the spirit energy orbs around the map. There are four kinds of items on the map: Life Cells, Energy Cells, Ability Cells, and the orange spirit energy orbs of varying sizes. You could skip some (all?) of the spirit energy orbs on the orginal because 100% map exploration didn't require them as far as I can recall, but on this one you have to nab every last one of those little buggers. For instance there are few during the escape sequence in the Ginso tree that you wouldn't likely get during the escape, so you have to revisit it when the coast is clear.
Also there are a few small rooms on hte map that you pass over and they won't have darkened areas over them when looking at the map, but you don't actually get credit unless you drop down into them (or jump up into them). There are a couple in Moon Grotto for instance that are very commonly bypassed by folks without realizing it, and it's difficult to know which one you didn't get credit for just by looking at the map.
Which area are you stuck at 99%?