V3's mesh shouldn't really have much to do with the boots, except to use as a "mannikin" to make sure the boots fit the way you want them to.

As for conforming, if the boots are "half on and half off", then it sounds like the joint parameters are wrong.

Here's one of the easiest ways to make conforming clothes:

1. First, find a pair of boots/shoes that already fit V3. Open its CR2 using Microsoft Word.
2. Near the top of the file, you'll find a line that starts with "figureResFile", followed by a pointer to the boots' geometry (a .OBJ file). Change that pointer so that it points to YOUR boots' geometry.
3. Now, scroll down a bit, and you'll see another figureResFile line; do the same thing here.
4. Finally, resave the CR2 with a new name. You just created a new figure, which should conform correctly to V3 :-)