Don't think I've seen wooden blocks there on the cross member before. I can definitely understand your concern for wanting the rear axle wedges. Initially, I don't know why your axle is angled up so high - I'd wonder if it were the original axle or if the saddle is in the correct position.
You state that you're trying to stay stock, so maybe all parts came with your jeep. I see an angle from the transfer case to the yoke but no like you describe. For illustration, from the SM, SM-1002-R6, look at fig 15 (lubrication), showing from above and fig. 277 (hydraulic brake system), showing a side view perspective. Neither show extreme angles at the yoke on the rear axle.
Something is odd. More details will help to figure this out.