Will clr or lime away clean the scale from inside the heater core?

Yes it will completely clean out your heater core. Make certain to disconnect you heater core hoses from the engine and purge the heater core of all antifreeze before you pour in the lime away. Leave it in for three hours then flush with clean hot water. Top the heater core off with antifreeze then reconnect the heater core hoses to the engine. Bring the vehicle up to operating temperature. Let it cool down for 15 minutes afterwards. Take radiator cap off. Turn vehicle back on. Run until operating temperature is reached. Then bring engine RPM's up to 2500 and hold for one minute. Do this several times until no more antifreeze come up out of the top of radiator. Then turn off vehicle. Put radiator cap back on then you are done.