Usually the longest axis is called "X", but it sounds like you're calling it "Y". A gear box will add backlash to whatever axis you use it on. Without seeing a picture showing how you plan to employ them, it's difficult to say anything meaningful about your selection of materials, but only the most rigid router-style machines are suitable for cutting aluminum and other metals. Any material will flex to some extent, but how much flex is tolerable depends on how it's used and what your tolerances are. If you really want to cut aluminum, then I'd suggest well-supported profile rails on all axes; round rails are too sloppy.