OEM manuals show the proper offsets when lacing wheels. I leave most of the front bolts loose except the top set of triple clamp bolts and the axle pinch bolts just slightly snugged up. I bounce the front end up and down a few times without the front brake on then torque all the triple clamps. I then bounce the front forks up and down again with the front brake on, torque the right side axle pinch bolts, then axle, then left side axle pinch bolts. I inspect the brake rotor to make sure it's not dragging and give the front end a close visual to make sure my eyes think it's straight too!
As far as your quarter inch goes I've seen tires where the tread pattern (Maxxis) is offset on the tire carcass by that much so it may not be wheel offset, bearing or a spacer problem just a cheap tire. I'd try checking the wheel spacing from the rim not the tire and see where you are at.
As far as how much all this matters and how much it effects handling I really don't know.