mistakes that are too often made by those with a philosophical background rather than the empirical sciences: the reasoning by analogy instead of the building and analyzing of predictive models

While there are quite a few exceptions, most actual philosophy is not done through metaphors and analogies. Some people may attempt to explain philosophy that way, while others with a casual interest in philosophy might not known the difference, but few actual philosophers I've met are silly enough not to know an analogy is an analogy. Philosophy and empirical science aren't conflicting approaches or competing priorities. They interact and refine eachother in useful ways. For example philosophy may help improve reasoning where we have only limited evidence, or it may help us understand the appropriate way for evidence to be used, classified or interpreted. It's only problematic when its used for social purposes or motivated reasoning rather than challenging our own assumptions.

I think there are certain specific instances where LW's dominant philosophical interpretations are debatable, and I'd like to hear more of what your objections of those kind are.

I now regard the sequences as a memetic hazard, one which may at the end of the day be doing more harm than good

I think just being wrong or misleading (assuming you think the main thrust of the sequences is problematic), isn't enough to be a memetic hazard. Otherwise we'd be banning all sorts of stuff floating around in books and the internet. I suggest memetic hazard ought to be things that are uniquely dangerous in leading to immediate harm to mental health (suicide, extreme depression or extreme aggression).