What would the hole locations be for a standard bravo setup in relation to the inner transom plate.

It's all adjusable, depends on where you want it tio come out, with stainless elbows and "S" pipes, and some exaust hose, you can pretty much put it where ever the best location is.
show us pic's of the back of your boat.
Larry

The holes are already there. I'm not sure if the old system was a standard brave setup. If you put a straight edge across the upper transom plate bolts and measure up to the hole centerline I have 4 1/2". 27 1/2" center to center.