Fletched arrows tend to go straight...it's the bareshaft arrows that plane....so make your calculations based on where the bareshafts land in relation to fletched. So if your bareshafts are landing to the right of fletched, you have weak shafts...as long as the shaft is not bouncing off the riser. A suggestion, tune nock height first, this will often minimize anamolies you see when tuning left/right first. Also check for nock tension, too much will often cause odd results too. I also wouldn't make any final decisions until you've tested it over a couple of different days...some days a feller is just "off" from his normal shooting form and doesn't really realize it.
As Bob said, if the bow shoots good with the .400 setup you mentioned, the .500 setup the same would be weak...as long as the arrow diameters are the same. The larger diameter of the shaft, the more it moves the center point of the shaft away from the sight window, in essence stiffening the arrow slightly.
I agree with the advice already given, fiddle with some lower point weight and see what happens before you cut.