I've developed a two-step process for prepping engine tin for paint.
The first step is to soak the parts for a couple days in my
heated parts washer, which will loosen the existing paint and I can remove what's left with a scotch brite pad.
The second step is to soak in a big plastic storage bin filled with water and CLR, 1 gallon of CLR to ~15 gallons of water. The CLR will dissolve the rust, but not harm the steel. I did a test this weekend, and it seems that it ignores aluminum as well: I soaked a VW bug/bus intake manifold for two days, which cleaned off all the rust, but didn't do anything to the aluminum heat jacket.
My process takes a few days, but I'm not in any particular hurry.