Thanks everyone for your replies. I re-ran the calculations with a different model based on your feedback. Which can be seen down below. The tolerances on the holes in both the axle flange and gear leg flange are very small, around -0.002. The contact points of both the bolt head and nut are perpendicular to the bolt axis(flat). Due to the small tolerances i'm thinking that the majority of the load (shear) is being applied uniformly along the bolt shank and the walls of the flange holes on both the axle and the gear leg. Therefore I'm thinking any moments on the bolt head and nut would be minimal.
The latest calculations show a 0.500 KPSI load on the center of the bolt, to deflect it 2.8 degrees (0.055in displacement) with a max shear force of 0.250 KPSI.
The NAS1304-29 bolts used in this joint have a min shear rating of 96KPSI. A 0.250KPSI pre-load seems negligible on the bolts, the flanges and the shim. The loads appear to be lower then I would have expected based on pure "intuition". I'm beginning to think that Van's engineering dept's position may be supported by the data. Unless my calculations are still way off