You can't get 100% in 5-1 - there are not enough bonuses in the level.
You can't get the gem in 6-1 - there is no yellow screwdriver in the level.

But you can cheat your way through:

In 5-1, when you collect all existing bonuses,
the first ones you collected will reappear at their old places (it's a bug)

About the gem - open readme.htm in notepad.
In the first line there are a bunch of 1s and 0s - in your case only one 0.
Change it into an 1 and save the file - you now have all the gems.