A bad bushing in the linkage or loose connections in the linkage. I imagine it could also be from within the tranny too, but let's not worry about that yet. I'd be sure that the linkage is bolted tightly to the car at the shifter, that the shifter is bolted tightly (but not too tightly) to the linkage, and that the bushing where the linkage bolts to the car is also in good shape - I'd recommend polyurithane if you're not already using that.

Congrats on the swap.