Use a straight piece of metal. A metal ruler works. We use the 12 inch ruler from a combo square. Place it against the rear gear and move the gear carrier until both gears are in the same plane.
As for damage, you’ve covered most of the options. What will wear out first is the rear gear and the chain. Keep the chain well oiled and watch for wear on the gears. If you believe that the gears have been misaligned for a while, start over with a new clutch gear and chain.
Tension the chain, snug the engine down slightly and rotate the axle slowly while watching the mid-point between the gears. At some point in the rotation, the chain will have its least deflection up and down. At this point you should have a plus and minus 10 mm deflection. Screw the engine stop up to the engine mounting plate and tighten down the mount. Recheck the tension. As the engine is tightened, the tension will change. Tighten slowly while watching the chain. Repeat until there is plus and minus 10 mm when the engine is tight.