I'm removing a wall between my kitchen and dining room which has beautiful 1X12 horizontal tongue n groove pine boards that I will have to cut through. I'm wondering how to finish off the cut end of the wainscotting. It will form an outside 90 degree angle with a non wainscotting wall.

Normally (assuming I'm understanding this correctly), you would cut a return, just like you would with molding. It will be a bit tricky because the major part of the boards are still on the wall, but with a careful, guided, cut with a circular saw at 45 degrees, it's possible. Then miter the trim strips and cut them on a table or sliding miter saw.