Hi,

the idea to take the figure's rigg as reference isn't so bad.
From your image it looks like the feet/legs are nailed on the floor and all actors from hip and above are moveable. If thats right I have a idea.

I don't have Brainy but I assume it has a normal standard rigging, e.g. hip, thigh, shin, foot, ...

So if you have saved your boots as a new CR2 there a two possibilities, I personally would prefer the hard way and edit the CR2 directly.

But you could do it a bit easier.
Only load you new CR2 and go to the setup room. Delete all unneccesary bones from the figure.
I guess that boots have at least rFoot, lFoot and maybe lToe, rToe. Possibly also lShin/rShin.
So all bones NOT covering a mesh group in your boots are useless. With one exception: leave the direct neighbors in the rigging. Thats for better joint purposes. All bones have a parent/child structure. So this means hold also the parents for a given child.
Easy example: Assumed the boots consist from toe, feet, shin. Than delete all bones except BODY, THIGH, shin, feet, toe, all in l(eft) and r(ight) version.

Go back to the pose room and conform the boots to the brainy. In Zero-Pose !!!
With the boots choosen go to the topmenu under figure if I am right by brain and check that there is NO IK activated. If that topic is not greyed out, you have IK-chains in your boots that are useless. Uncheck the respective entries. And now save the boot-CR2.

Normally it should work the correct way now. If not it's best to open the CR2 in a text editor and search directly for inkyChain and delete this parts.

But as first try to have all reduced to the necessary bones.

Otherwise you should also have a look to the tutorials of PhilC www.philc.net/tutorialsIndex.htm
or of Dr.Geep drgeep.com/NPU/NPUWelcome.htm .

Good luck
Jo