You want to buy 'Parsing Techniques 2nd Ed' -- this book is fantastic and will give you the understanding and clarity you seek. It is wonderfully comprehensive.
And schmitz' thesis is an excellent read on tools and techniques to deal with ambiguity http://www.lsv.ens-cachan.fr/~schmitz/papers
and the non-canonical parser that results is quite interesting too :-)
PEGs vs Boolean Grammars: I think adding negation and conjunction to a grammar is the same as positive and negative lookahead
PEGS + Ambiguity: Like other people, I solved this in my last top down parser by attaching both precedences and relations to terms
i.e E[50] :== E[< 50] + E[<= 50]
so you can force a left or right associative operator.
That said, although determinism is nice, I think ambiguous parses are inevitable once you have a sufficient level error handling within the parser
parsing theory is pretty developed and established but in reality many parsers are cobbled together top down parsers.
you can't use existing parse libraries to handle HTTP for example.
(That said, yakker is an approach with earley parsing to handle data dependent grammars)