It is very hard to check this assertionn because State by state breakdowns of presidential voting are organized by county, not by congressional district. Nevertheless, I tried my best a few years ago to analyze such a scenario.
Without a doubt, Bush wins, and it isn't even close.
I believe that if this system (Nebraska/Maine) were in place nationwide, Republicans would have a lock on the White House that would last until the Democrats change their stripes.
So, you're wrong, no way Gore would have won.
County by county Bush slaughtered Gore but the high number of votes in New York and Cali, along with an unusually high vote in Florida, probably went a long way toward giving Gore the popular vote.