any time you cut a board its going to change it a little bit.you definitely want to cut a wood core, hopefully not cutting thru any carbon stringers although it can be done.
the best way is with a waterjet or maybe some kinda star trek laser
. i've never built a diy split but from what i understand most people use a circular saw with a straight-edged jig (a board) clamped to the board as a guide.