I follow the new workflow for the Holy Grail using LRTimelapse 2.2.1 and LR 4.3. But when I'm done I still see some jumps, so I want to back and fine-tune some of them.

What's the right way to do this? Which steps should I repeat and which should I not repeat? I couldn't find this addressed in the eBook. I think I have a pretty good idea of what is happening at each stage regarding LRTimelapse writing & reading to the .xmp files, but I'm not getting the results I expect, and I think I'm doing something wrong. Perhaps I'm repeating a step that I shouldn't. Thanks.

You can always go back to Lightroom, fine tune your "jumps", save Metadata for the keyframes and then repeat the second workflow row in LRTimelapse: reload, auto transition, maybe deflicker, save.