I spent about a year making changes.
Some of the more difficult changes included the map system (markers, tracking what parts of an area you'd seen, etc), widescreen (the original version was 4:3... this involved lots and lots of code changes and a lot of map editing), a built-in help document (that grows as you go through the game), automatic map hints (this involved adding new content to the maps).
There was a bunch of other stuff too, like subtly redesigning levels to make some puzzles easier to solve etc.