I had a freeze plug go out on my 90 Dakota 3.9, 290k miles. I pulled the engine because it was on the back of the passenger side head against the firewall. I decided to do some work while it was out including replacing all the freeze plugs with brass, oil pump, oil strainer, timing gears and chain, intake gasket, exhaust manifold gaskets, valve cover gaskets, front and rear main seals, water pump, and thermostat. Decided while it's on the lift I'd also do upper and lower ball joints and inner and outer tire rods.
When I pulled the freeze plugs I discovered the bottom end of the water jackets it was full of "mud". I don't know how it wss cooling. It took several hours to get clear water to come out of the engine. What causes this?

 

Age, not changing the coolant as recommended.... or even using the wrong coolant. Pretty typical on an engine of that age though.

 

^what he said and using straight water as coolant. That is what the insides of steel or galvanized water pipes look like after a decade or two. It's just corroded metal that came off a molecule or two at a time.

 

I'm hoping to have it back together in the next 2 weeks. First time I've had to do more thana Easter pump on a truck I got for $700 14 years ago. Great truck.