Just went through the same with my 92 YJ, W/P, thermostat, hoses. There were no original issues just thought it was time for some preventative maintenance. As yourself my expectations of getting the system clean fell short of reality. Had the radiator out flushed the system with water until it was clear. Was going to have the radiator boiled out and pressured tested but found very few shops do that work any more. So I preceded to flush the radiator until clear water came out. Next day did the same, Hmmm, rusty water again, next day flushed again with same results, this process went on for a few days with rusty water initially every day. Finally spoke with an old timer who used to rebuild radiators, his advise was, quit messing with it before I do need a new radiator, what I was seeing is perfectly normal and install it. Long story short, did install with hesitation, filled it up and to my surprise the coolant is clean and green. I know what your feeling, anything short of perfect is disappointing, but sometimes it is what it is, otherwise you will end up losing sleep, your "Jeep Joy" and in debt. My thoughts are, do the best you can (now be reasonable), be proud of your work and most importantly "ENJOY", not everything will be perfect, that is what it is all about.