When you have overlapped the corresponding vertices you can select all of them by choosing to turn on the Xray view of the model and by using the box selection option to draw a marqee around all of them at once. Type B and draw a rectangle only around the pairs of vertices you want to merge. Then select Mesh > Vertices > Merge. Note that the mirror side of the model mimics everything you have done.

Xray view

For the Wolfie character I chose to model the head in a separate Blender file to reduce the immediate complexity. As with the body, the head was a simple cube, subdivided, extruded, and otherwise fine tuned until I was satisfied. Mirror modeling was also employed, but I did not apply the modifier. I wanted to append just half of the geometry to the body so I could merge the whole character after welding the head to the neck.

In the file containing the body of the character, in Object mode, I chose File > Append, and selected the head object from the Objects folder of the file. The geometry was imported, and I shift-selected both the body and the head and typed Control-J to join them as one mesh. Now in Edit mode I could weld the head to the neck just as I had welded the hand to the forearm’s wrist.

Welded

In the file containing the body of the character, in Object mode, I chose File > Append, and selected the head object from the Objects folder of the file. The geometry was imported, and I shift-selected both the body and the head and typed Control-J to join them as one mesh. Now in Edit mode I could weld the head to the neck just as I had welded the hand to the forearm’s wrist. When I had finished welding the head to the neck I applied the mirror modifier, which merged all the corresponding vertices of the model and its mirror.

I could now add another modifier, Subdivision Surface, that would smooth out the entire model. The modifier has multiple levels of smoothing for both the view and rendering, and I used the default values. I added a hat as a separate piece of geometry just for fun.

The model was now ready for shading, animating, and rendering!