New user. I have a 2003 Civic 1.7l Vtek. Head was warped and had overheating issue. Head machined and lasted for 1 year before overheating problems reoccurred. Managed loss of coolant 2nd time for a few months by avoiding freeway driving and only driving locally topping up radiator before/after each short trip. Mistake made was using tap water.

Bought new head and just did head replacement. Also decided to change out all cooling system components. Inspection of T-stat manifold, water pump, and all visible water passages shows heavy mineral deposits, presumably from hard water used. Suspect I need to do a complete cooling system flush but need to use a chemical that will breakdown the mineral deposits. Would like to do this BEFORE I install the new rad.

Can anyone recommend a procedure to chemically flush the engine without using the old rad (still in place but disconnected) or the new rad since I don't want to clog the new rad with the removed deposits? Also, should I remove the T-stat when flushing both with and without running the engine? I considered flushing with distilled water and CLR or ZEP (calcium, Lime & rust dissolver). I used ZEP with a brush to clean the deposits from the T-stat housing and then soaked/rinsed in water to neutralize the acid. The bottle does not disclosed what concentration or type of acid but it does say not to use on aluminum and other metals. No idea if it will harm seals hence this request. I also have a generic coolant flush but suspect this will not touch the mineral deposits. Also think this may only be useable in a cast iron block not an aluminum block.

New head and water pump are currently installed but still need to instal intake manifold, alt, PS pump, rad, fans, etc.... Was planning to replace the rad and hoses last and now that I see how much mineral deposits are present I need to do a serious chem/treat and flush.

I've seen a post suggesting to use a dishwashing soap pre-flush followed by a citric acid flush from a Mercedes procedure. Also a suggestion to use vinegar but nothing confirming either of these treatments are acceptable for a Honda engine (aluminum, seals, etc.). Bottomline, I don't want to reassemble without trying to remove the scale/deposits as this may be the original problem that caused the overheating and head warping-both times.

Appreciate any advice that won't make my problems worse!