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OK ta - that's more or less the approach I've taken, glad I'm not missing anything then!
It just seems odd as looking at the caliper, the pads don't seem to sit in the middle of the gap (i.e. the rotor almost touches the caliper body on one side, when its roughly centred between the pads). I have it so there is almost no noise and it's not stopping the wheel spinning, I guess the tiny amount of contact will stop with a tiny bit of use now.
If the pads are in correctly they should be aligned to the caliper, then, as you say, unbolt the caliper just enough to move it side to side and look through it onto a light surface and gradually tighten each bolt with it held in the right place, I find giving it a spin and listening helpful too with the final adjustments done with one bolt tight enough to not really move and adjust the other, then swap and tighten.