It was good to catch up Mark! I need to make a trip out towards you so we can do some wheeling together!
Or... Steven Sasaki and I were talking and agreed we would lead a 4Runner-run on next years Rubithon. It hasn't been officially announced, but I guess I'm letting the cat out of the bag. Hopefully you can join us!
As far as trimming your frame... It's really only the fat area at the bottom of the IFS frame that needs trimming. Your lower links will hit.
You could leave the rest of the stock frame, though you might end up doing a little trimming if your panhard bar interferes with your frame when passenger tire is stuffed. I don't feel like your box is too low.