Your alignment between your motor end of each screw and bearing end need to be exactly in alignment. The best way to do this no matter what the material (mfd, aluminum etc) is to drill your motor center mount/bearing shaft end mount holes at the same time by clamping the parts together and drilling together. If you have a design to make the bearing/mount adjustable, then do so. You can even overside your motor mount holes slightly to allow a little adjustment.
You also may have bent screws. Roll them on a piece of glass (like a glass sliding door) and any bent shafting will show up. Take time to carefully straighten any you notice out.
As far as couplers, get some cheap flexable couplers that will eliminate slight misalignment problems. I wouldn't recommend welding anything to to your shafts or screws as the heat can also cause warping, or in the case of the motor shafts, damage to motor seals or bearings. If you're on a budget, something as simple as a 2-3 inch piece of stiff flexable hose/tubing (like fuel line for autos) with the correct inside diameter as your shaft/screw and a couple of good hose clamps will work. On my first machine I just epoxied the piece of tubing onto my cheap allthread "screw" and then double clamped the other tubing end to the motor shaft... it never came loose or slipped.
Good luck!
-marc |