So, you are following the 96-98 guide, but yours is a 99-00 Civic, and the system was redesigned. In the 96-2000 FSM, the instructions for the 96-98 and 99-00 heater core are in separate sections. Dunno yet if that makes a difference.
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See my car's mod & maintenance thread and my electric bicycle's thread for ongoing projects. I will rebuild Black and Green over decades as parts die, until it becomes a different car of roughly the same shape and color. My minimum fuel economy goal is 55 mpg while averaging posted speed limits. I generally top 60 mpg. See also my Honda manual transmission specs thread.
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