At 48", you can go either way - screws or rack-and-pinion drive. If it were me, I'd keep those rails long and buy some other ones for the Y axis; short rails aren't hard to find, and you'll find the extra work envelope comes in very handy for projects you haven't thought up yet. For a 96" span, rack-and-pinion makes more sense than a screw. Many people like to drive the longest axis from both sides to avoid the "stuck drawer effect", but it's not strictly necessary. You only have to use aluminum for moving parts like the gantry (and not necessarily even there); it's a waste of money for stationary parts, where steel not only is cheaper but works better. That t-slotted extrusion that's so popular is especially expensive; it's light and fairly stiff but hard to justify on a budget build, unless you don't have the equipment to deal with other materials.