My MC when I acquired it appeared as if it was running swamp water in the cooling system, it was all really rusty looking with some black gunk floating in it, and stank!!
So I'm thinking ok I definitely am going to need a water pump and a good flush, then I got thinking weeeell maybe I should flush it out using the old water pump first,
rather than run all that rust through the new water pump.

I bought a bottle of Radiator flush, however I am curious as to if it would pay to use some CLR or other such bathroom rust cleaner, to clean the rust out of the system
I can't see how it would hurt anything, and am curious if anyone else has done this?

 

I myself don't use chemical flush in my cars , IMO they do more damage than good. On these cars there's a few different ways of flushing out the nasty from the system if you have access to a garden hose and don't mind doing a little extra work. Start with the heater core , remove both heater hose's off the engine and flush water both ways thru the heater core. Put hoses back on and install a flush T and flush the engine. If the system is as bad as you describe remove both radiator hose's off the engine and do the same as you did with the heater core, flushing water in both directions and then refill system. If you haven't done a thermostat now would be the ideal time to install one.

 

Well Jeff, I did buy the thermostat, but haven't put it in yet, a lot of this aluminum shows corrosion so I thought I would do some dress up, and either wire wheel the aluminum and paint it since there do not seem to be many dress up kits for these engines. Last time I worked on it I pulled the tensioner off, so I will flush the core as you suggest, and I'm going to wire wheel the tensioner and probably paint it, there are tubes in it that run the coolant from the pump to the core so I will clean them out as well. I will also probably replace both radiator hoses and wire wheel the T-stat cover and paint that. I need to find some high temp paints.maybe even powder coat, but I'm leaning toward high temp paint.

 

I'd X2 just using water to flush it out. You're never going to get 100% of the stuff back out that you put in, so I'm always leery about putting all kinds of random chemicals in there.

The other thing is you should take a look at the coolant to see what's in there. If oil or trans fluid are getting mixed in, you'll need to correct the leak or itll just get like that again.

 

The oil is clean, so I'm not worried about that, the trans fluid is kinda black so I am worried a little there, but I dont believe there is a coolant leak there, and I'm rebuilding top half anyway, but the cooling system seemed to be just old nasty rusty swamp water. Trans fluid will be the first thing I do after I get it to run again!