About the toe bones: the boot mesh probably has polygons for rToes and lToes.

One of the rules for Poser boning is to always include one bone extra; you should keep rBigToe1, lBigToe1, and probably one of the other toes too (each foot), to prevent the end point of the rToes and lToes bones to snap to the origins of rBigToe1 and lBigToe1.

These toe bones will NOT have geometry assigned to them!

Another option would be to assign the toe polygons to the foot. Then you can leave the children of the lToes and rToes bones out.
The endpoints of lToes and rToes will probably end up in the wrong place - one of the peculiarities of the Setup room.

Another option, maybe even better: strip the bones you don't want using CR2Builder. Just keep the nodes collapsed, and delete all entries you don't need.
After you've done that, expand the figure node and delete all weld statements for bones that do not have geometry.
Also delete all addChild statements for the bones you have removed.
The advantage of this method is that CR2Builder will keep the endpoints of the bones in place, unlike Poser.

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