You sure can use CLR to flush the engine and heater core, I pour the stuff in the rad and drive it around all day or 2, then flush it out. If it was green before, its going to be rusty orange now! Just make sure you use your garden hose to flush out the engine, heater core, and rad real good before refilling it all back up.

I unhook the heater hose that comes from the waterpump and pump the water into that hose, so it goes into the heater, back into the block, and out the hose where the waterpump is. Then flush out the rad real good too. Run the water till its coming out clean. Unhook the fat hose of the bottom of the waterpump and it will drain about 95% of water from the block, that is the lowest point in the cooling system.