You have given no real information, you are spouting off basic technical information but none of it explains anything and it comes off like you are trying to make it sound like your job is important and you are smarter than the people you work for.
You have said they are axle housing that weight 200-300lbs (that is a big difference in weight considering the drawing probably has the weight on it), they have tolerances of .002 and .003 at different spots but later you said the variation is .0001. You mentioned that if you can get 6 good pieces shipped back there is a $500,000 to be made, either that means those 6 are worth $500,000 which sounds more like military equipment, mining trucks or cranes, or the contract is worth $500,000 if you get it which doesn't seem like much money for the effort that seems to go into this. I doubt the housing is worth that much, so your company is probably doing the full axle assembly, or maybe you are confused and it is actually a gearbox.
Is the alignment you mentioned where the variation is or is it a bore that is off, the bore that needs to be within .0001 would most likely be for a bearing which makes sense. You haven't mentioned the material either, is it a cast iron axle housing?
Material makes a big difference in the case of thermal expansion, do you even know that it is thermal expansion? The stresses in the material could cause the diameters to to creep after machining and they could pass tolerance after machining but be out of tolerance by the time they get to your inspection.
You haven't mentioned how the surfaces are machined, are they ground or honed? For a variation of .0001 to mentioned the parts would need to be inspected in a climate controlled room, even the heat from someone touching a piece of metal causes it to expand by more than .0001.
It all comes down to you not even trying to find a solution here because you aren't even given any details, or any of the steps that have already been taken. You are just trying to prove you are an engineer by talking about stuff that it doesn't even seem like you understand.
You are asking in wrong part of the internet, there are forums that if you gave proper information people could give you legitimate feedback but it appears that you lack basic problem solving and communication skills to describe the problem with the required technical information, you spent more time talking about the drama with your company than the problem.