I doubt you need to modify the body side brackets.
When you buy a new cross member from Ford Racing M-5059-A, it's adjustable. Meaning the cross member is not welded up to the bushing sleeves.
Once you install it on the car and slide the cross member to where it needs to be, bolt the trans mount to it, you tack weld it into place (crossmember to bushing sleeve).
https://performanceparts.ford.com/do...htM-5059-A.pdf