Squirrel,first you need to space the hub so the sprocket carrier lines up with the front sprocket, as the front sprocket is fixed by the engine. then make a spacer up for the other side so it fits snug in the swingarm.
It doesnt matter where the disc sits (as long as it doesnt foul anything) as you will be having to fabricate caliper mounts to suit anyway.
Not all hubs are centrally aligned with the rim, they can be offset to the left or the right (this offset is called dish)however they are stronger when central,all pushbike wheels with 7,8,9 speed gear cassettes are dished to allow room for the cassette.
You need to work out where the rim needs to sit to be aligned with the front wheel (and work out where the rim is, in relation to the hub fixed in the swingarm) and then get the hub laced to the rim with the correct amount of dish, which a good wheel builder can easily do.
If it is not quite right the dish can be adjusted be tightening the spokes on 1 side of the wheel then loosening the spokes on the other to pull the rim across.(im not suggesting you do this yourself but you can take back to wheel builder and say the rim needs to be 5mm to the left or right etc).
