The analogy of 2000 is much better than 1960. The JFK/Trump comparison does not fit very well. The only things they have in common is their interest in lots of women and the status of a billionaire. Thus JFK won the PV, though very narrowly.
I seem to recall a situation involving Alabama's votes putting the nationwide PV vote in doubt. Basically votes were counted for Kennedy that should have gone to an indy Dem slate or something like that.
Sort of. In 1960, the Alabama Democratic Party split between Kennedy loyalists who supported the national ticket and those who favored a slate of unpledged electors who could then act as kingmakers after the election. The compromise reached was to nominate a split slate, with half the electors pledged to Kennedy and the rest remaining unpledged (these electors ultimately voted for Byrd). This makes it hard to know who won the popular vote in Alabama that year, because unlike most other states, Alabama's electors were chosen in eleven separate races: instead of voting for the Democratic slate or the Republican slate, voters had to go through and vote for eleven electors, and could divide their votes however they wanted. This raises the question of whether you count votes for the Democratic unpledged electors as votes for Kennedy or as votes for Byrd; the latter gives JFK the state (and a slim plurality in the popular vote); the latter leaves Nixon as the winner on both counts.