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I just finished doing the same last week. I did all of the flushing (VC-9 followed by many interations of distilled water) prior to installing the filtering system. However, I couldn't get the final flushes to be clear until I installed the DieselSite filter system. Those final washes were grayish - like weak tea. I think there was some sort of sediment or something clinging to the coolant passages because once I installed the filter and drove for about 20 miles, it cleaned right up on the next (and final) flush.
So to come back to your question - do most/all of the flushing prior to installing the filter system.
I would also add that you do the install while you have the system drained, that way you won't make a mess or waste any new coolant. I cut into my coolant lines after draining out thru the stop**** and lower hose, so nothing spilled.
2005 F-250 (stock), CC, 6.0L, 6-speed manual, 4x4, 150K miles (CAT ELC coolant, Dieselsite Coolant Filter System, Blue Spring, BulletProof EGR, Ford OEM reman injectors, ScanGauge II)
2006 Kawasaki KLR-650, 9K miles
1995 Kawasaki Concours (ZG-1000), 31K miles