The first pony could be named Gadget if she discovers how machines work, if she just discovers how the world works in general then her name could be Sofia (the Greek word for wisdom). Just a thought but having a book, scroll, and a list makes it sound like she has three cutie marks unless this is essential to the plot you should choose just one.
For the pegasus Open-Heart sounds good.
As for the third pony, having two cutie marks has an air of mystery about it and she should maintain it. Since she makes potions and magical equipment I would have her known as "The Tinker", and then maybe have her name revealed toward the end of the fic.
In the mean time you will need to find an editor to give critique and advisement. If you want you can send me your rough draft of the first chapter or two so I could look it over.