[Woodclaw]

1. keep in mind that Hero Lab is just a way to keep track of what you do, if you want to rule that when choosing Toughness as the save it set the difficulty higher just do so
2. using the editor you can do that, but keep in mind that the validation rules are based on the core books, if you want to modify something to fit you own HR pay attention
3. Super-Speed is composed of 4 elements, Speed, Quickness, Improved Initiative and an Array, all the Special Alternate Power are part of that array and cost 2pp/rank, if you add Autofire to Rapid Attack you bring its cost to 3pp/rank or more and it won't fit into the array. Anyway you can alway build an Alternate Power and select it with the Special Alternate Power option from the menu
4. Speed and Quinckness aren't PLcapped, you can buy them at any rank you want.
5. As far as I know there isn't, since the modifier from the enhanced version are either temporary or they can be negated by a Nullify effect, while the base save can only be drained but not negated