Well since nobody else is responding,
I don't really have a definite answer, this is a strange problem. I'm just going to throw a few ideas out there. Hopefully it'll be better than nothing.
Check the clearance between the ring and pinion, looseness here could cause a clunk.
Maybe the syncros weren't installed correctly. The lack of grinding means the syncros are engaging correctly. The syncros are there to control the freewheeling speed of the gears so that the gears are slowed down to the speed needed to mesh with the next gear. If the syncros aren't fitted to the gears correctly, they can't control the speed of the gears correctly, and noises occur.
Did your mechanic put in the correct weight gear oil?
Hopefully you'll figure it out. From the lack of response, i think everybody else is stumped as much as you are on this problem.
good luck, and let us know what the problem was when you figure it out.
Mike
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