Originally Posted by Uniblurb
Hopefully you have your heater set to high when flushing the system so it goes through the heater core. Also helps to back flush the core and disconnect your hoses at the front/right of the valve cover rather than possibly damaging the soft copper tubes coming out of the firewall. When I replaced my AC evaporator I also replaced the heater core and while I was trying to be careful I could not get the hoses off of the core w/o bending or half-crimping these soft copper tubes. Didn't matter since was replacing the core anyhow.
No need to worry about the heater setting, the heater core is always at full flow, what controls the amount of heat is the blend doors in the plenum. Agree with back flushing the core, also, check the heater hoses for crunchiness, just squeeze them, if they crunch, slap new ones on, corrosion tends to build up in them, in my 97 they got so bad that the heat wouldn't work, I replaced them, flushed the core, and all was good with the world, and my coolant stayed cleaner also,