Well first off I'm glad to hear you got your heat back---the reason I told you to bypass the heater core was because you have been working on the symptom, not the cure. The rust in your heater core came from your block, not vice-verse, so if you don't clean out the block first, then it will re-pollute the heater core and you'll be doing this dance again.
But since you bought the kit (good move) and you're comfortable with the idea of back flushing, you should proceed and clean out the block.
If I had not told you to bypass the core while cleaning out the block, all the junk from the block would have lodged in the core, possibly so much as to be incurable.
I feel confident that what I told you to do was correct, not wrong at all.