I would be suprised if it's an issue with the chassis drilling, mainly as they are CNC cut and drilled... not much to go wrong there, not saying it doesn't happen though. The chassis holes should all be the same distance from the centre line, that goes for the suspension blocks and the bulkheads... it's part of the clever flex of the 416
As for the suspension blocks, first you need to measure is the distance between the screw holes. They should be the same. An easy way to make sure they are lining up is to bolt the two blocks together, just take a couple of screws and go straight through one and into the other (keeping the flat sides against each other). If you have any misalingment between the two, you'll find it there.
If there ok, well... there's not much more you can do. Try swapping the blocks round on the car too, giving F/XA (3.5 deg toe out). If it's something on the car, you should see it reversed, with 4 on the right, and 3 on the left.... If it's still the same sides, then it's probably the setup gear.
HiH
Ed