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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, 140K miles (CAT ELC coolant, Dieselsite Coolant Filter System, Blue Spring, BulletProof EGR, Ford OEM reman injectors, ScanGauge II)
2007 Ford Freestyle Ltd, 90K miles
2006 Kawasaki KLR-650, 9K miles
1995 Kawasaki Concours (ZG-1000), 31K miles