when you loosen the clamp and fit the tool you need to wiggle the engine bay linkage to ensure its centralised, then tighten the pinch bolt. Also check for play in any of the bushes in the bay, and look at your relay shaft bush closely. any play here and it will make aligning the gears especially hard.
if the tool fails you, the way i do it is to loosen the clamp bolt till it can be moved with a little force. then select 3rd in the car, and wiggle the stick left & right till its just about in the middle. Then try 1st, 5th and reverse. If its not right put it back into 3rd, tweak it and retry. Once happy that all gears can be selected, tighten the pinch bolt.