Running boards are not be altered to fit, unless you are welder or a master mechanic. The reason I say that is because of the nature in which these are used. A lot of load is placed on them at different parts of the board and the last thing you need is for them to fail when the load is on it, aka your body weight. So dont drill holes and make it fit. You could grab used OEM running boards for about 100 bux anywhere with no problem, so spend the money. The rest are just 10mm bolts and you can just get them from anywhere for next-to-nothing or just get it from the vehicle it comes off.
Yes they do have pre-drilled holes on the bottom and they run all along the bottom of the cabin/body. If they are 6" shorter, then it means they are not meant for this vehicle (unless they are nerf/tube bars) and it will look crappy. Shaving 3 inches off on each end will be a nerf bar and not a running board.