I’m glad you asked this. The Jed that I knew had mixed feelings about Spiritual Autolysis. For all that it is held up in the books as the ultimate practice, as far as I know this idea came from the actual authors/editors of the text, and not from Jed. Jed supported anyone attempting to make use of the practice, but he recognized that it’s very difficult to do well. I know you've had some dialogue with Jed about SA already, and gotten some of his ways to cut through to the heart of the practice, but let me add a bit about how I think it works.
Mostly, what people do in the name of SA is the equivalent of journaling, and in fact that’s what’s demonstrated in the books. Journaling can clear the mind, or it can further clutter it. It can be a tool of discovery, or merely a way of recycling and rehashing mental activity. Journaling is not really what SA is about.
If you want to get closer to the real point of SA, it helps to remember that the idea came from Descartes and his Meditations. Here’s how he started his first “Meditation”:
“Several years have now elapsed since I first became aware that I had accepted, even from my youth, many false opinions for true, and that consequently what I afterward based on such principles was highly doubtful; and from that time I was convinced of the necessity of undertaking once in my life to rid myself of all the opinions I had adopted, and of commencing anew the work of building from the foundation.”
Pretty bold, right? He then gives some suspect reasoning about why he waited until he was so old to make the attempt (though he was only 43 when he started - ha!), and says:
“Today, then, since I have opportunely freed my mind from all cares and am happily disturbed by no passions, and since I am in the secure possession of leisure in a peaceable retirement, I will at length apply myself earnestly and freely to the general overthrow of all my former opinions.”
That is spiritual autolysis - the systematic overthrow of all the nonsense that has come to comprise your world-view. You interrogate absolutely every belief to see whether it’s actually true. And the punch line, of course, is that none of it is.
Descartes’s basic tool of skepticism was that everything that seemed real to him could be an illusion spun by a malignant demon trying to trick him. There just wasn’t much sci-fi around in Descartes day, or he would have gone on about simulations and implanted memories. Instead he went supernatural and decided that no matter what tricks that demon was up to, there was still some thinking being (Descartes himself) having the experience of being tricked. Cogito ergo sum: I think therefore I am. That was the only thing he could be sure of. At least it was until he got into some nonsense about the necessity of God’s existence (with a capital G). He was, after all, a creature of his culture and his time.
Your job as a universal skeptic (more universal than even Descartes managed to be) is to try to find something that you can know is actually true. That’s the reason for the exercise - to be rigorous enough in your questioning to try to discover the difference between Truth and everything else. To not stop until you get there.
As for your starting point about suffering. I am personally certain that you aren’t suffering. Not because we can get all non-dual and say there’s no “you” there to suffer. Even if we imagine there’s a you there, that you isn’t suffering.
Something is happening. That’s for sure. That something seems pretty unpleasant, and you’ve learned to interpret the something as “suffering”. But you want to find out what that something is really made of. What is occurring that you’ve learned to call “suffering”. Pop the hood and look inside. Really dig around in there. What’s it actually made of? What can you know about what’s actually happening and why it gets experienced as “suffering”.
Question every answer you come up with. Is that really what’s happening? Could you break it down even further? Can you discover an interpretation that is at least more “truthish”?
As you mentioned, logic can only get you so far. Coming up with an intellectual answer won’t be satisfying for very long, unless it dramatically alters the nature of the experience, or of the experiencer. That’s how you know when you hit upon some Truth!