Thanks for this, this solves the issue for me.
Obviously now the bones are mapped, the rotation issue can be solved in the edit pose menu.

It is probably possible to fit parts of Standard CC base mesh onto non-standard body with Shrinkwrap modifier (if non-standard is a human).
I said parts because fingers and toes most certainly would not work with Srinkwrap and should be cut-out from the source mesh, or masked before applying a Shrinkwrap.
But torso, legs and arms should be no problem as long as you preliminary match Standard CC base onto non-standard with sculpting.
Some addition sculpting/smoothing would require after the "wrap".

thanks, a lot. any ideas or youtube video on how to replace just the body with my sculpted body and leave the head well alone?

Yes, it would be a lot easier to morph/sculpt body as needed rather than struggle to make face morphs with Humanoids.
Humanoids are only good for something that is quite impossible to make from CC base characters - like animals and other oddly shaped characters.

I see.
I have a couple of stylized exagerated muscular body meshes. I think it'll be easier to replace cc4 body mesh with my stylized body mesh. That way I can retain cc4 blend shape, visemes and all that. What do you think?

Not unless you create face morphs in CC4. You can spend time in Blender and rig the face with a dozen of bones and then use them in Face Profile Editor to make morphs.
Or you can rely purely on "soft" morphs where you'd create them in Blender and import as OBJ into Face Profile Editor one by one.
It is very time consuming process. If you intend to make an Extended face profile morphs + Visimes, you are looking to create close to 170 morphs.
It is also possible to create batch and import as FBX sequence.

https://www.youtube.com/watch?v=ebgsHfYjCyQ
https://www.youtube.com/watch?v=A-4lGCu76Sw

I'm in the process of rigging my own character with the metarig in blender. Taking longer than expected because i'm rusty, lol.
I was wondering if the face is well rigged, when I import the character into cc4, would I be able to use the face puppet and expression tools?

In most cases a leaf\end bone does not do anything.

But for some odd reason and unlike 3DXchange (CC4 predecessor), the CC4 armature in the view-port would not display an end bone in the chain.



You can still try to assign it from Bone Manager (even if the last bone is not "visible" in the view-port) and it would probably work. Though I did not try.
I just find it odd and inconvenient that last bone representation is missing in visual and we have to go through the list to look for it.
There should at least be a check box somewhere to show/ignore end bones in the view-port.

hmmm, why, what does the leaf bone do? I thought it just makes the armature look messy.

The bones are visible in the bone list, but don't seem to be assigning from this.

When you export out of Blender is "Add Leaf Bones" option checked in Armature? Make sure to check it.