First: Breathe. You're rushing waaaay ahead of yourself. Congratulate yourself on learning the kana. That's step one.
Second: Don't try to reinvent the wheel. Educate yourself on how to educate yourself. Read the posts on this message board. Go to alljapaneseallthetime.com (people just call it AJATT here) and read what Khatz has to say about how he learned Japanese. Gather as much info as you can, and figure out what suits your style the best. You aren't the first person to ask this question, so you should be able to find some good ideas out there.
Finishing RTK1 will take some time-- anywhere from 3 months to 1 year, depending on how fast you try to go. There's a bit of a split in opinion on whether to learn Japanese language/grammar at the same time as you do RTK1. It's really up to you. If you feel you HAVE to learn some JP grammar, grab one of the textbooks people recommend. (A lot of folks like Japanese For Everyone, I liked Genki I and II pretty well.) There are discussions on books for beginners all over the message board.
I like the idea of using kana-based graded readers if you can find them, just to keep your kana skills sharp. The more kana you read, even if you can't read the kanji, the better you will be able to read it down the road. It really is about practice and immersion, in my opinion.
I wouldn't worry about kanji chains until I was close to not only finishing RTK1, but also had 1600-2000 cards in my 4th pile. But that's just me. I started worrying about RTK2/chains while I was at ~1000, and it got me distracted from the task at hand.
What to do next depends a LOT on how you learn, and how much time you're willing to put into learning Japanese. (It also depends how long you can focus on RTK each day with your sanity intact, and without burning out.)
Come up with a plan that you think will work for you, but be willing to CHANGE it if it doesn't work for you. And don't skip a day. Ever.
Edited: 2008-01-18, 1:51 am