Clunk at low speeds

So my car has always had the infamous 3rd gear grind, when shifting into it at high revs. (which seems to be gone now ironically) Recently I had a new axle put in on my passengers side, and now when I am going slow if I shift at all there's a clunking noise. For example: ill be going 40, depress clutch, run through the gears, no clunk. Slow down to 30, running through gears, there's a clunk. Right before I come to a halt (maybe 3mph or somehing) the clunking goes away. I never drive the car hard and always shift in <3000rpms. Any ideas?