Thanks for these questions. (1) The cases under rule #2 are a mixture of proclitics and common words (such as the two conjunctions and the adverb ou). Most proclitics (including most prepositions, and most forms of the definite article) in fact do keep their accent, so a general rule can't be given. Since enclitics do follow set rules, which are much more complex than simply not having an accent, they are given their proper treatment separately in the last (and most tricky) of the rules!

(2) Analysis by morae, whereby a short syllable counts as one mora, and a long syllable as two, generally allows the rule that an acute cannot go back more than four morae, and a circumflex more than three morae - but you still have to deal with the fact that, as you say, a final long restricts an acute to three morae from the end, and face the exception given in n.13. So we decided to avoid it entirely!