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it needs to be fitted parallel to the seat stays right?
More or less. Strictly speaking, it should be aligned so that the plane with the drill guide hole in it contains the wheel axis, but a few degrees either way doesn't matter. The jig is made to guide a 5mm pilot drill and then flip over to guide the 6mm finished size, using the shank of the 5mm as an alignment guide while nipping up the clamp.
Might struggle to fit it in the gap