Letterworks,
Yes, thanks for that. I had actually made the fall off zones encompass the whole shoe and the outer one bigger than the inner. I thought that would be all I needed but it is not. I don't really fully understand the relationship between "falloff zones" and "joint angles" but I needed to also adjust the joint angles to exclude the shoe as well.

Lululee,
!!!! Thank you !!!!
Whilst I had seen PhilC's shoe converter and the tut you pointed out I had ignored the info, thinking that it was not relevent. You pointing me at that tut ticked the final box and it has all fallen into place.

So. a recap of what I have found

1. Using the default V4 for bone donation is right out! She is not zeroed and it just messes things up terribly.
2. Loading V4, zeroing her, turing off IK and saving her into the library to use as a bone donor is better but still not perfect. Loading her back in and checking bone angles in detail  reveals that she isn't actually zeroed. For example her foot angle comes back as 0.002955. Now, that is very small but it seems to all add up and slightly mess up the whole process.
3. V4 development foundation doesn't have foot (or hand or head) polys so using that to export and use as a tailor's dummy to model shoes etc does not work. However, a zeroed model of V4 exported as OBJ is fine.
4. After the new content is made, import it into Poser and use the V4 dev foundation as a bone donor
5. Shoes (especially ones with straps or tall boots will need careful adjustment of both sperical fallof zones AND joint angles in order to exclude the shoe from being deformed.

Okay. That's it for now as far as I have got. This was fine for zeroed shoes. Next stop, high shoes or flat shoes and how to conform those.