I flushed used thermocure and flushed my coolant system really well back in January until in ran clear. I went through a lot of hose water, distilled water, and then fresh coolant. I drained drained the radiator last week (in June of same year) and my coolant was looking kind of grayish and there is black bits floating around in it. The black stuff is sludegy, not hard. I sent some coolant to Blackstone for an analysis and they said there was no trace of oil or engine exhaust and that the coolant was fine, as far as coolant goes.
I think the best thing for TJs and their rust prone blocks is just to do a bleed and feed every 6 months to a year. A bleed and feed is basically just draining the radiator and refilling it. If you do that periodically enough, the bad stuff gets diluted enough to stay fresh. You can buy a gallon of concentrated prestone and a gallon of distilled water for well under $20 so it doesn't cost much. It takes about 2.4 gallons to drain the radiator and refill.
The black stuff was probably one of your hoses breaking down. You should give your hoses a squeeze to feel for soft spots before it bursts on you. If it were me, I would change all the hoses if I saw black sludge in the coolant.
Most modern coolants have a 5 year/150k mile change interval. I use Zerex G-05 that was specified for a 2006. The older green coolant has a 2 year/30k mile interval. If you have green antifreeze and you are flushing the cooling system and changing the hoses there is no reason you couldn't upgrade to Zerex G-05 at the same time to extend the service interval.
Jeep 4.0 blocks are no more rust prone than any other engine. There is no need to drain and refill the radiator every year.
You have to remember, when you're on this forum you are dealing with internet autists that have ass burgers about the Jeep TJ.
Does it make a difference whether or not you get every last bit of rust out of the engine block's coolant passages when you flush it?
No, not in the real world...
In most cases, the only thing flushing the coolant system instead of simply changing the coolant accomplishes is satisfying an obsession.