I don't know if i can help but... I'm assuming that you are using a jack to hold the diff up? If not, it will help while aligning the holes. Back a year ago or so, I was talking to Mike and he did say that he had a few that he had to replace because something was off so i don't know if that's happening again. I would make sure that the diff was supported on a jack first. i'd remove the horizontal bolt that goes through the diff arm support and don't put any of the vertical bolts that support the diff into the frame of the truck. Loosen the bolts that hold the diff drop in place. You kinda have to make sure that the diff drop is in place before sitting the diff arm and bolt into the diff drop otherwise there may be some force that's causing something to be skewed. After the diff drop is in place with the 4 bolts, then tighten that down, align the diff with the aluminum spacers in place and try to thread the bolts (vertical) into the frame and then lastly connect the diff arm onto the diff drop. This part you may have to wiggle to get the bolt hole to align.
In the first pic, you have the diff arm bolted to the diff drop before the four bolts that hold in the diff drop are in place. I think this is where the problem is. I could be wrong. This is what i'd do. If this still doesn't work, i'd call mike. Hope this helps some.