Update: So it seem Occam's razor prevails once again in that the apparent cause of the noise was a dislodged bolt in the drive shaft causing it to knock against its surroundings. I drove the vehicle hard on the way back home and couldn't get a concerning noise to emit so I think it's fine for now. The shift into second seems considerably better now so I consider the issue at hand resolved for the time being.
Thank you all for your thoughts.
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