Debugging
It looks like the reason for the insidious chain rub is the swingarm attitude. It’s flatter than in its original setup. Compare these pictures, starting with a detail of the donor bike.
A horizontal line from the pivot intersects the swingarm about 2/3 of the way down. On the Longshot the intersection is lower, passing almost through the dropout:
The effect is to raise the rear axle, lifting the chain line to the point where it hits the frame. So the question is how to push the axle back down? I could move the seat post back, but that would be an offensive amount of work and disruption. I could make new upper shock mounts, increasing the standoff to rotate the swingarm around the existing pivot. It would work but doesn’t feel right – that junction takes a lot of stress and with the increased length any alignment error would make it prone to bending. I could move the main swingarm pivot closer to the seat post. The angle of the shock would be slightly steeper but I don’t think that’s a big deal.
There’s more thinking to do, but moving the main pivot seems like the best alternative.