Sounds like you can't drop the back of the wishbones down far enough to achieve the caster you want? If you really need to cut a section out of yours to make it work, there is no rule of thumb, every car is different. I would block it at the ride height you envision the car ultimately ending up at, and then take only enough out of the wishbones to make the back end line up with where you are going to mount them.
I would also put some gussets on the cut portion to reinforce them after you get done welding them back up. These radius rods weren't all that thick when new, so anything you can do to make them stronger is a good thing.
Don