I did basically the same thing. Once I got the wings in the jig, I clamped in the front spar and moved the rear spar as needed as I checked the alignment/twist. Once the spar was in the right place, I clamed it down. I hung a plumb bob at each end of the wing and one at the middle of the wing. I also ran a fishing line across the front spar to make sure I didn't have any sag.
I did my aligning without the skins on. Once I had it where I wanted it and clamped in, I skinned it and the skins went on nicely. Every so often, I will still check my plumb bobs and fishing line to confirm I still have no twist and/or sag in the wings.