If it is actually the flange then the only way to fix it is replace the flange and yoke or get rid of it. Have you tried flipping the yoke 180 degrees to see if anything changes?
There are open u-bolt yokes for the AAM axle but the take a 1480 joint rather than the AAM 1485. I am not sure how trying to mate those together would work for efficacy. That is usually done in conjunction a custom 5" drive shaft with Spicer joints. It is almost impossible to tell if the vibe source is the DS balance, harmonics, flange alignment, or a combination thereof.
My truck was little easier to diagnose. A lot of was the steel DS and center support, the 1 piece OE DS solved a lot of it but not all. Since I could never get the rear diff seal to quir leaking figured it had to be something with the flange and it was. A custom DS from Texas and u-bolt yoke stopped the pinion leak and smoothed all the vibes.