Conversions are always a pain in the butt. The easiest way to fix the broken up vertices is to go into vertex mode, select all the vertices, try using weld selected threshold at 0.01. (in Edit Mesh it's the 0.1 thats right next to Weld->Selected, in Edit Poly, it's the box thats right next to Edit Vertices->Weld). That should get the vertex count down to normal. (if it combines vertices that it shouldn't, use a smaller number).
Also if you use polygon mode normally, you'll want to remove the unnecessary edges. The easiest way to do that is to go into Edge mode in Edit Mesh, then select all the edges, and finally Surface Properties->Auto Edge choose something like 6 instead of 24 [for the angle], then click Auto Edge. It's not 100% fool proof, but it'll get rid of a lot of unnecessary edges. If it gets rid of some that are actually required, you should be able to go into Edit Mesh->enter Edge Mode, select the edge and click Surface Properties->Visible.