A few tips
Hi there Pi Seas,
Reading over your post, I think I might have a suggestion, but it partially depends on how you're working on this.
From what you say, it seems like you're trying to make a master list of your projects, and then write all the actions that make those up. Is that correct?
If so, I think part of the challenge is that you're trying to work top down. For me, one of the reasons that GTD worked so well for me was that it was more of a bottom up system. I'd never been able to be consistent on a top down system, as the day-to-day seemed to take over before I could get things going.
So my suggestion, at least for the initial setup, is to try to work a little more bottom up. DA's suggestion for implementation in the book worked for me. The short version of it is get your inbox, collect all your stuff into the inbox, and then one by one process the items, deciding ONLY the very next action that needs to be done on that item.
After that, you'll have a "master list" of your NA's. If this is the master list that you mention in your post, then you already have done what I said above, but the next part may be different. Now it seems that you're trying to organize these things based on project.
I would do two things here. First, remember that your Action Lists are to be divided by context, not project. So look at the master list and grab those things that will be done at work, at home, etc. Now, everyone's contexts vary to some degree, but the good thing with GTD is that it is flexible. Start with some contexts that make sense to you now, and if you need to change them in a few weeks, go for it. Then you learn more about how YOUR system will work and how you want things structured so you can GTD as well.
The second thing I would do would be to review these items and see what projects they relate to. Basically, it might be easiest, at least at first, to populate your project list from your action list, rather than the other way around. If you go PL into AL, you might end up with a lot of new NAs that are related to your projects but don't take into account any of the info you've already process from your collect and process phase.
After these two steps, do a quick review. Take a look at your project list, see if there's anything you feel is missing. Are there any projects on there that aren't really active, or are for a later date? Move those to Someday/Maybe. Now that you've reviewed the projects, take a look at the action lists. Is there at least one NA for each of your active projects? If not, remedy as necessary.
From that point, then it becomes more maintenance and tweaking. Those initial steps can be a little confusing and time consuming, but once they're done, you have a starting point. It's like sales. It's a lot cheaper to keep a customer than earn a new one, and with GTD, it's a lot easier to tweak a system to fit your needs than to get it going in the first place.
And I know this post has been ridiculously long, but one more tip. Try to do this in an uninterrupted setting. Even if you have to spread it over a day or two, if you can get this done without interruption, then you're not having to move backward in the process. Once the system setup is done, then start working on what has come in while you were setting things up.
Once again, sorry for the long post, and I hope this helps!
Adam