My question before I get started is should I go with two motors for the Y axis?
That really depends on the design, but for a typical moving gantry machine, two motors usually makes a more rigid machine.

Can I use any length ballscrew?
Typically, you either get a screw to fit the machine, or design the machine around a screw. It's kind of difficult to use a 48" screw in a 24" machine.

What size machine are you looking for? What materials do you plan on using to build it?

After doing some searching I now know that I want to use linear slides and ballscrews with some hefty stepper motors.
If by "hefty" you mean big, that's often a poor choice with steppers. On small to medium sized machines, smaller steppers will often outperform very large steppers.