Hey Jonathon,
I got tripped up looking into the remove doubles feature. But thanks to a google search it was easily rectified with the replacement action. For me the W key no longer Brought up that menu either but the Non-Clicking Mouse Button brought up a similar menu.. But the replacement action is called Merge-By-Distance (correct me if I am wrong) Alt +M and then B. Selecting a distance like 0.00001m should do the same action.
Regards,
Blanchsb