The rules were ignored because the rules were incomplete and often contradictory. Florida's election law was a mess.
And to your point about flawed ballots - why were there so many flawed ballots in the first place? The answer is because the technology stinks. It's easy to say that people must punch it out all the way, but the system was rife with potential shortcomings. That's the issue.
I'm not sure what W's lead has to do with this - I've not mentioned partisan results at all.
What is clear from Florida is that a) their laws for elections suck, b) the didn't have substantive recount procedures in place, and c) the punch card technology is very poor.
Compare that against the Minnesota Senate recount in 2008. Since the vast majority of Minnesota uses connect-the-arrow optical scan ballots (a system that is far more intuitive and error-proof than butterfly ballot punch cards), determining a vote in a hand recount was easy. Likewise, Minnesota's procedures for recounts were set in stone and reviewed in advance, thus all of the requisite poll workers were prepared for the entire process. There wasn't any of the legal scramble or competing standards that you had in Florida because Minnesota's laws were far more clear on exactly what to do.
I'm just not sure what you're trying to say here. If you want to argue that electronic voting machines are unnecessary and potentially problematic, you could have picked a far better example than Florida, 2000 to make your case.