Don't think you are doing anything wrong per se. You ARE putting in a chassis with a rear suspension of a design that the body was not made to accommodate. So no surprise you'd need to do some surgery. When you are doing the body mods, make sure to leave enough clearance so you can remove those upper control arms should the need ever arise.
Just adding adjustable rear control arms (inboard heims) to my S1 required the removal of the battery box corners due to the design difference.
It's good to be comfortable with basic fiberglassing techniques if you own an old Lotus.