I replaced the heater hoses that connect into the firewall this weekend and both the inlet and outlet pipes had TONS of scale inside and out. I wirebrushed the outsides before putting the new hoses on. The scale is just caked on the insides of those pipes. Should I be doing a doing heater matrix flush / back flush? What to use?

 

you can try back flushing the heater core, usually has limited success. remove the heater hoses and just use a garden hose, blow the tap water out of the core after you done.

 

That same buildup is in your radiator waiting for summer to blow the head gaskets.
Check the cleanliness of all other hoses too. The engine block will have its share of buildup also.
I would say a very agressive chemical to dislodge such is to be planned in above freezing weather instead of coolant, for enough miles to do its work, and repeated treatments.