You probably didn’t do anything wrong.
Zbrush and OBJ scale sometimes does this. Unless you’re modeling to a precise scale, just manually correct your meshes until their almost exactly the same size and use project-all.
Without a detailed examination of your mesh, I’m not sure where your unwelded verts are coming from, but it is likely (IMHO) that there are some unwelded points in your highres mesh, perhaps from the original base mesh you used.
In Zbrush, the Import sub-pallet will have options for merging and welding (Mrg and Weld buttons.)
Given that this might be the case, when importing into Maya, it’s important NOT to merge points as you will change the point-count/order at that time.
Since you have this annoyance (varying point counts), the solution I suggested above (using Project All to transfer the details to your new UV’d base mesh) will likely work. Just scale up your new base mesh to the same size as your current highres mesh once its in Zbrush (Project All depends on the meshes being almost identical in scale.) The maps (normal, displacement, etc.) you generate will be the same when applied the base mesh you had Maya as long as you keep your UVs consistent between the base mesh in ZB and base mesh in Maya, regardless of the scale in ZBrush.
HTH,
-K