If you have the head off I would just flush it out well with a garden hose. I had a old 50's (AC) diesel tractor that looked like the coolant was mud. Quick flushed it, as much as I could, to get the crap (slug/mud) out. Then added a bit of dish washing soap and continued flushing until it was clear.

If your concerned about more than just the block; like heater, rad, water pump; then of course you will either do more extensive part removal and/or flushing.

I've never done the diesel fuel flush but typical engine flush is with engine running. I don't however believe that this would have been sufficient with the situation I had in the tractor.

I always use distilled water when refilling the coolant. But that my just be my idiosyncrasy.