I assume here that the transmission is in gear keeping the first split gear still while you twist the second section of the gear into alignment.
Right about here, where you feel the gear turn to line up, I would try tapping on the tool or a solid part of the base plate with a rubber mallet. Perhaps while twisting with more and less force. Resist temptation to use a five pound metal hammer.
Another thought. Measure the distance that the plate is falling short of its mate.
Does this distance correlate with something else?
Measure the distance from the base plate to the advancing face of the second section of the split gear, and compare that to the distance of the base plate mating surface to the alternator drive gear.
I would think the distance is the same. If not, it may indicate another obstruction.