I know i always flush mine out whenever i replace anything. I always crack the bleeder before pressing a piston back in place and let the fluid escape that way instead of pushing the crap back through the system.
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'96 slt cc 2wd, #8 tst plate,215's,3k gsk,4"exhaust,afc modded,14.5*,new head,rebuilt auto w triple lok tc & shift kit,rebuilt diff,riderites w/onboard compressor,triple pillar boost,egt,tranny temp,402k km,305hp 686 ft/lbs