After more reading and more thought, I've decided to stop lupin-feeding (raw or cooked). The following article (a PDF) describes a study in which growth inhibition and other problems appeared even at 10% inclusion levels among broiler chicks. ps.fass.org/cgi/reprint/80/5/621.pdf Apparently some of the problems disappeared after dehulling or heat-treating, but the retarded growth and some skeletal abnormalities remained.
It just goes to show how widely you have to research if you're a layperson trying to formulate a ration on your own. The net is brilliant, but unless you know the right key words, you can end up googling the same old same old. It took me hours to find the above study and it seems very clear that lupins shouldn't be fed to chicks in replacement of soy. I wish I'd been able to find more information when first looking into lupins, as the basic agricultural information suggests that it should be perfect in replacement of soy.
I can however look back over the two years spent on this project, and see that some of the issues I've tended to ascribe to genes or to mealed feeds like meat meal may have in fact been due to lupins. The study in the above link suggests that there may be unidentified toxins innate to even sweet lupins that cause systemic effects in young birds.
Obviously I feel pretty bad about this. I've gone outside 'the lines' in trying to formulate my own feed, and with the best of intentions I've in fact been unwittingly cruel. But I feel to give up on the whole home-feed project and go back to fulltime commercially formulated feeds would only be a shift, not a fix. Remember that my reading on artificial methionine hit on studies that showed other forms of health damage (cardiovascular disease, fatty liver, etc). Artificial additives abound in commercial feed.
What I may do now is review my whole diet and try to reach my protein goals differently. I still don't want soy meal because I won't be able to avoid genetically modified soy (unless I find an organic producer). But exactly how I'll manage the protein levels I want without using lupins or soy is a bit of a question right now.
Give me time, give me time. Apologies to anyone who has taken the lupin feeding experiment as a guideline — hopefully you haven't taken it to an extreme. But my birds appear healthy generally so I feel a change in diet will remove any of the setbacks I may have caused — I hope this is true of yours too.
Best wishes everyone, and I hope I can find a new way to keep my chickens natural.