If you really want to get deep into flushing that cooling system, look at Cummins Restore Plus cooling system flush.... this stuff will pretty much peel off any internal cooling system contaminant lol.
However, you could be in a situation that you'll need a new rad because the system is too clogged up.
In this instance, I'd also recommend that you replace the water pump and the thermostat, and go OEM whenever and wherever possible.
Also, did you put a "T" in the bypass hose so you could ensure you got the heater core into the flush equation?
You could also have to consider a heater core replacement as well in this equation.
Being that you've had real dirty coolant coming out, I'd seriously consider a new OEM rad cap, too
Do it all once and then you don't have to consider the "what if's" down the road!
Change your coolant moving forward every 3 years or so... regardless of the mileage! It is a chemical that starts losing its redeeming properties in its third+ years of service!
This is all just my opinion though