If you use an orthogonal camera and set the Document Display Style to Outline, makes it easier to check if the joint centers of the feet and shoes match. You can use the Joint Editor on the feet, then Paste into Background, then select the shoes to see if they match.

Parenting the shins of the shoes to the shins of the character, BEFORE conforming may help. If not, I think the following procedure is worth a try, but no guarantees.

Construct a pz2 with the relevant scaling, and using all the joint parameter channels from your modified figure, from those actors which are common to the shoes. Also include the 'endPoint', 'origin', and 'orientation' lines from near the end of each actor. Inject this pose into the shoes, BEFORE conforming them.

The theory is that if the shoes have exactly the same joint parameters then they must bend in exactly the same way. Because the shoes are slightly bigger than the feet, you may still need to tweak the size of some of the falloff zones slightly to encompass all the polygons in the shoes, but it should at least put you in the ball park.