I believe you are looking to change the fluid, as you cant flush a diff. A flush intercepts a system fluid circulates (not saying a diff doesn’t, but read on) and uses the pressure of the system to exchange the depleted/contaminated fluid with fresh fluid. Good examples of a flushable systems would be transmission (auto), or cooling system. Anyways, you are on the right track with addressing all the rust and the hard to get to areas while the motor’s out. It’d be a good time to check out brake lines, steering rack, etc. DEFINETLY give that engine bay a firm once over seeing as it’s empty,…make it clean, because emptiness is loneliness, and loneliness is cleanliness, and cleanliness is godliness, and god is empty just like…Billy Corgan,