I understand the confusion; in a perfect world it wouldn't happen. This is a case where reading through the chords, watching a video of the bloke playing the stuff, and fifty years experience helps slightly. I can't say why the partitions are wrong, and it's just bad luck, I reckon, that it just so happens that that's the ones you've chosen to follow. Don't be dis-heartened, though; not all transcriptions are wrong, and kudos for having at least tried to work it out yourself (all the more so as I'm certainly not a Neil Young fan, myself, and don't 'get' the appeal ...).