I love Heisig's method, but as you can see, it's extremely devisive. What I did was go through the book, write each Kanji down once, come up with a story in my head and move on. On the same day, I would then go through the cards in Anki, using one of the premade RTK decks. All I see on the cards is the keyword and from there I "draw" the Kanji in the air and then see if I was correct.
However, I don't think putting the stories on the front of the card is detrimental at all. People say it's too easy, but I don't think they get the point. Whether something is easy to do or not doesn't change the effectiveness at all. If you can draw the Kanji from the story and repeat that the right way often enough (which is what the SRS helps you do), then that's great. At some point the stories will fall away on their own. I haven't found the need to "wean" myself off them, it just happens naturally, no effort required.
Here's my Anki graph if you're interested in my study habits:
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The "relearn" ones were because I didn't realize how to use Anki the right way and so I kept pressing the "good" button while learning new cards, pushing them back 4 days, which was too far. I could've been a bit more efficient had I not done that.
Anyway, you can see that I went pretty fast. Most people don't like to do it that way and take maybe three to six months to go through the book. I think that is fine, too, however, I have found that it gets easier to do the more you do at once, since Kanji keep reinforing each other because they use the same elements again and again.
Edit: Here's an up-to-date graph after I finished my flashcards today:
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