Down & Dirty: The Plot To Steal The Presidency is an inside account of the Florida election debacle of 2000. The author, Jake Tapper, reported for Salon.com, was very close to the action, and delivers a detailed chronological analysis of those two months when America watched and waited for Bush or Gore to become the President-Elect.
Tapper has plenty of negative things to say about both Democrats and Republicans in the recount struggle. I've had to revise some of my opinions of the mess. For instance, it's not clear that the statewide undervote recount (that the U.S. Supreme Court decision halted) would have resulted in Gore overturning Bush's lead.
You've got to look at this problem as one of signal vs. noise. There's always noise in any vote gathering system (though particularly with punch cards). "Counting all the votes" i.e. determining the intent of each & every last voter is not possible. It should be completely up to each state, county, or local canvassing board that, when asked to do a recount, they decide whether to do it at all, and (if so) the methods that they will choose.
It is clear that the Supreme Court's majority opinion was one of the worst in modern times, that the equal protection argument was bogus. Tapper points out that at least one conservative writer has put aside partisan loyalty and acknowledged this. But the end result, of stopping the swirling madness and going with the certified result, was probably the right thing to do. If the lead were reversed I do (now) think that the Supremes would have made the same decision (by the same flawed arguments). The Constitution ultimately gives the State legislature the power over choosing electors, so it's likely the result would have been the same in any case, given the Republican dominance there.