The best way to clean your heater core is with muriatic acid. This was in a TT writeup by Mark Whatley several years ago. I have used it on a few heater cores and radiators with excellent success. I believe muriatic acid is what rad shops use.
You can get a gallon of it at the hardware store or a pool supply. It is HCl - hydrochloric acid - you DO NOT want to get this on you or anything nice you own.
You have to pull the heater core, put it on end, fill it with muriatic acid, and let it sit for a few minutes. Wear gloves, goggles, face shield, long sleeves, etc, etc.!!!! Do not breathe in the fumes and don't hover over the core unless you like choking!!! Nasty fumes come up when the deposits inside your core start dissolving.
I usually dump the excess back in the jug of muriatic acid and rinse the radiator or core well with water.
By the way, you can't run it through your engine. It does not react with brass or copper (hence the cleaning abilities) but does react with aluminum (and will thus eat your intake).
-Tyler
Today and yesterday, the temp. was -39 celcius here. I just don't drive my cruiser on these 
