IMHO, the problem was that any competent statistical analysis of the punch card ballots would prove that there was massive ballot tampering by Gore operatives and the purpose of this excercise was to pre-empt a serious investigation. The disturbing part is it almost worked and there is no penalty for voter fraud, even though Gore and company almost pulled off a successful coup via punch card ballots and other means of voter fraud on a nationwide scale.
Gore won approximately 600 counties out of 3000(Bush won 2400), yet he supposedly "won" the popular vote. If that doesn't fail the smell test, I don't know what does.
Quick reality check here:
The number of counties won by Bush and Gore has no relation to the popular vote in itself because counties range in population from a few hundred to millions. There is also no correlation between the population of a state and the number of counties.
Gore won the most heavily populated urban counties by wide margins while Bush won most of the least populous rural counties.
An interesting statistic, to be sure, but hardly indicative of vote tampering.