This is a bit of a pet peeve of mine, but... I'll try to be brief.
I'm not a fan of Heisig at all.
I'm not a fan of any method that involves learning large amounts of kanji as nothing but shapes and English "keywords" (calling them 'meanings' is misleading) -- I think this is one of the best ways to completely waste your time as a beginning student of the language, and will do you little or no good in the long run (assuming that your long term goal is to be able to actually read Japanese, and read it the way a native speaker would -- i.e., not just 'decoding.')
You'd be infinitely better off learning a set of 500 kanji or so, but learning them _well_, and by that I mean not just "meanings" and readings, but also learning commonly-used compounds, and learning them in context, so that you're actually building up your vocabulary (in a meaningful, practical way) and reading skills as you learn.
I would recommend
Bonjinsha's Basic Kanji Book to start with. I wouldn't be surprised if all of the JLPT 3 kanji are in there, but I couldn't tell you off hand (I never wasted my time with JLPT 3.)
Basically, what I'm trying to say is that learning kanji just to learn kanji is pointless. If you don't connect it with actual reading practice right from the start, you'll just be spinning your wheels.
That's just my two cents.