But that's the thing, I measured from surface to surface (wing gap along the line of the struts) so any discrepancies in strut length or attachment points wouldn't matter. It's also a bit surprising that the rear strut would need to be raised 3-4mm to correct the 1 degree difference.

But I'm sure you're right that it's probably a number of tiny misalignments that are adding up.

*****

So disregarding any prior length measurements, I took the practical approach of "try it and see." I added two M2 nuts under the bottom of the rear port strut (in effect lengthening the strut by 4mm). And I cut off the previous incidence wire. Took new measurements with the incidence meter which showed 0 on both top and bottom. Finally added a new incidence wire (with minimal tension). So I've finally got 0-0 on both bottom and top wings...even if those nuts aren't very attractive. At this point, I don't care. I suppose I could slap some black paint on them.