Rust on the head does not mean there has to be rust on the thread. There are better things for threads than ACF50 as well: plain grease or anti-seize last longer, but adjust torque as above..
The bolts are rusty because what little anti-corrosion plating was on them has now gone - cleaning them will only open clean steel to the elements and that won't turn out well, ACF or not. You could look at a systematic replacement process with stainless, or look into re-plating with zinc. You can buy kits over here that give you the basic plating setup & I've had some good results with it.