From reading your inital post, I would advise you look closely at THIS ;
http://www.seymourduncan.com/products/electric/humbucker/medium-output/jason_becker_pe/
I'm by no means an expert, but my path has led me down a similar SEARCH of tone as yours, and so I've been doing some reading up on the Duncan website.
The higher output Custom leans more towards the metal spectrum IMHO, and doesn't lend itself ideally towards what you are looking for , because its tigher and more gainey than for waht a lot of the stuff you play needs, although it is a workable option IMO. The Lower output Pearly Gates and/or AphII Slash, as well as the Whole Lotta Humbucker are also a very possible solutions, yet are geared to heavy Blues rock and Classic hard rock and old school metal, which could do what you want almost entirely, but wouldnt get you into the territory of 90's metal, and I think you might miss that more thank you think?
Yep, the perpetual Burn is a my candidate for our tone search. I actually think Duncan had the first idea for this evolutionary pickup and another company was was so impressed by the Perpetual Burn, that they decided to issue their own version with a guy by the name of Gilbert endorsing it, but I'm probably wrong.