Have you even bought one of these arms, yet?
If you have, then you would notice something really quickly: The motor gearbox housings form the structure of the robot arm; they are integral to the design.
Some of the steppers you propose to use are larger than the gearboxes housing the motors on the arm itself (the arm isn't that big). Heck, the shafts on some of the steppers are larger than some of the gears in the gearbox!
You already say you don't have an understanding of electronics; this project is -not- a beginners project. Nobody has yet even managed to implement position feedback on this arm using the motors as-is (a requirement for the system you propose). You may be on a route to frustration.
Lastly - what is this "scanner" system supposed to do? Is using a multi-degree-of-freedom robot arm the best solution? If it is, and precision is needed, you are likely to find it better to purpose build the robot arm from scratch, and not try to convert something like this toy. If you must use something off-the-shelf, a commercial robot arm (while insanely expensive, even used) is going to be the better solution.
You need to, however, learn the basics of electronics, robotics, motor-control, feedback theory, etc - before attempting something this advanced. Otherwise you are going end up throwing a bunch of money and time at a project that is only going to end up frustrating you and your bank account...