I know that the first place to start is right behind the TB,where those two walls are at the bottom of the plenum.This is the first time I have had my plenum off where I can see the inside of it . There is a hole on each side on the back ramp of the part that needs to be ground down.I assume it is like this on all plenums and when I grind this down,possibly elongating these holes, that this is not a problem,right?

 

Those are the EGR holes. The ramps are supposed to create a pressure differential that helps scanvenge the gases. If you just grind it down flat you shouldn't have any problems.