Brought figure in from MakeHuman added a few bits then joined the mesh. Used Rigify and rigged the mesh. All seem to go to plan but as you see from the pics I have missed something. Workupload File Here
I know the question is somewhat old, but I'll add an answer for the next person finding this.
It is unneccessary to do the rigify rigging manually, as that is supported by the rigify functionality in the recommended import path for makehuman (MPFB). With MPFB available, you can import a MakeHuman character either by simply opening the MHM save file (new human -> from presets -> import mhm) or by using the socket import (new human -> from makehuman -> import human)
For more information on MPFB, see http://static.makehumancommunity.org/mpfb.html
For rigify you have two options when working with character meshes:
Option 1 - import with game engine rig and convert
First select the game engine rig in MakeHuman and equip any set of clothes, hair and body you want. Then import to blender using either of the methods above.
With the rig selected in blender, you can now find the "convert to rigify panel":
If you accept the defaults and simply click the "rigify" button, you will get a fully rigify-rigged character including clothes.
Option 2 - Set up character and rig in MPFB instead
If you want a full rigify rig including the face bones, the game engine approach will not suffice. Another option is then to do the modeling and rigging MPFB directly, skipping the MakeHuman step.
Create a new human (new human -> from scratch). Then go to the rigging panel and add a rigify rig:
This will add a meta rig to the body.
Add any other meshes you like (eyes, clothes...). They should be automatically rigged and weight painted.
Once satisfied, you can generate the final rigify rig from the same panel:
This way you will have access to most of the available functionality in rigify.