So I only recently discovered Heisig's method, but I want to do it fully. Before I discovered it I signed up for an intense 12 week Japanese training program and then immediately afterward the whole class will be going to Japan. I anticipate little or no time to study subjects of my own choice (Heisig).

So here's my problem. I am on kanji 600 right now so I can either continue learning each one as I have and get a concrete story in my head and only go over about 800 total or I can go through the rest of the book quickly so I'm familiar with all of the radicals before I start the class and before I go to Japan. (I'm going for two years)

Thanks for your help!

Here's what I think. I'm only at about 613 right now so I'm not the #1 expert or anything. First of all, you should continue to do your reviews, or you will lose what progress you've made. The spaced repetition will divide up what you know from what you don't, providing good time management on what to review. Secondly, 12 weeks is a long time. If you only did 16.6 per day you would finish 2000 at the end of 12 weeks. In my opinion, you would be better off spending a little bit of time doing Heisig / RevTK than in whatever the intensive program would have you doing. Actually, there's a chance doing both will help each other, except that you may be too burned out to do Heisig. But I would encourage you to at least keep up with your SRS reviews and then add new cards. Shoot for 12 on bad days and maybe like 30 on good days. I would also contemplate putting stuff from your intensive course into a separate SRS such as Anki on your computer. I honestly think that courses like that will be in one ear and out the other, after the quiz is over and they move on to the next chapter, but that's because I'm biased. (I'm kind of a blind follower of http://www.alljapaneseallthetime.com and he's pretty anti-classroom language learning. If you haven't seen the site, take a look at it. Short version: Create an immersion environment, listen to 10,000 hours of enjoyable Japanese. Input is more important than output. Do Heisig to learn the Kanji. Learn the kana. Then start putting authentic Japanese sentences into an SRS. The sentences should have ONE thing you didn't know and want to learn. After 10,000 sentences you'll be fluent.) I'd love to know more specifics about the program if you have a link, especially if they have a page that explains what's good about their program and what their learning theory is. Are they planning on teaching you all the Kanji in the class? The whole class is going to Japan, and you'll be there for 2 years. Is the whole class going to be there in Japan for 2 years doing the same thing? What are your plans exactly? Obviously when you are in Japan you're going to want to continue with your literacy, pick up where you left off. You'll be able to walk into stores and buy books, magazines, manga, newspapers, etc. in Japanese. I'm so jealous.

12 week intensive course with a 2 year Japan stay? That's awesome.

Last year I did a 10-week intensive Japanese course which covered the entire 2nd year of University teaching (at a school that prides itself on going faster than other schools...is this true? I don't know...But my professor wrote IJ, so it must be OK).
What I'm saying is that you're in a similar boat as I was.

If I were going into an intensive course again this year, I would definitely not stop my Heisig studies. I found that the homework didn't take too long, studying was easy, and I had a lot more free time than I originally thought.

You might have kanji-intensive readings and kanji quizzes -- but don't let those daunt you. If they're "irrelevant" kanji (ones you haven't heisig'ed yet), just write in furigana. For the quizzes, you already know heisig's method of making stories -- it's not hard to come up with "temporary" stories. I did this before I found heisig, which is why I found it so amazing when I found it. 解 -> The colorful, powerful cow jumped over the moon. The primitives aren't correct, but I remembered it.

I say go and do heisig. Even if you do 10 a day, that's still 840 kanji in 12 weeks.
Heisig shouldn't be too long, hard, and grueling for you. Especially because your going to Japan, I think you should know as much kanji as you can (even if it's only just a vague meaning of it).

Okay thanks. You guys really did help.

The program is a mission trip thing for college aged kids. We all go learn the language and then we go to different areas of Japan to interact with the people (i.e. do service, teach english, and preach the gospel). I'm going to the Kobe, Japan area and I'm really excited.

I see. You're going to be around a lot of people speaking English, though, it sounds like. It might end up being easy to cling to the English side of things. Are they going to be preaching the gospel in English or Japanese? If you had the ability to read out of a Japanese bible, that would probably be pretty useful for you. There was another thread on here where I posted a link to a bible in Japanese, in PDF files. Maybe figure out some key verses.

Yeah that would be a good idea. I'm hoping to learn as much Japanese there as possible so I'm planning to use every opportunity to preach in Japanese. We'll be in pairs for most of the time except for at conferences when we all meet together so I'm hoping most of the contact I do have will be in Japanese