Use the existing classes as a guide. Aside from the Nature questions it should be pretty straightforward, and you only have to worry about nature questions if you’re adding a new species/race. If you notice, the skill lists all have a pretty similar distribution. Also, because skills advance with use the starting values will kind of even out after a few adventures unless you do something crazy. As for class abilities, you can either ask them to pick one of the existing classes to follow or you can mix and match a bit to create your own theme.
Yep. The humans and half-humans don’t have new Nature questions, neither do the dwarf and halfling classes. But the Dark Elf, Sea Elf, Minotaur, Gnome and Roden do.