Historian Garry Wills has suggested that Adams would have won the Election of 1800 if the 3/5ths Compromise didn’t exist. I’m assuming that’s true.
Assuming that is true, I’m assuming it’s also true that Jefferson would have still won the popular vote? If so, would most of the southern that won the presidency have then won the pop vote but lost the electoral college?
Questions: Is Wills correct? Would TJ have still won the PV and lose the WV? Would then Madison, Monroe, Jackson, then have also won the PV and lose the EV?
Does a chart exist of the Electoral Votes by states comparing the numbers with and without the slave population?
The "popular vote" in US presidential elections doesn't really tell much on a national level really until the 1820s.
Before then, states had very different franchises, and in terms of Presidential elections, very different manners of choosing Presidential electors. Only six of then-sixteen states had electors chosen in any manner by voters (interestingly they were mostly Southern states: Virginia, Kentucky, Maryland, North Carolina, Tennessee and Rhode Island). All other states' legislatures chose electors for that election, with those legislators themselves getting voted into office in various constituencies over the course of the year. The manner of choosing electors changed in most states from one presidential election to another, and most states didn't settle on a first-past-the-post state wide awarding of pledged electors until the 1820s (South Carolina held on to state legislators choosing electors until the Civil War).
It's also worth pointing out that as this was before the adoption of the Twelfth Amendment in 1804, each elector actually had two votes for President, with the runner-up in electoral votes becoming Vice President. This is why the 1800 election was actually decided in the House of Representatives, after Jefferson and Burr tied the electoral vote.
A final important point to keep in mind is that until the 1820s, voting was subject to state laws restricting the franchise to property owners (interestingly, in the case of New Jersey this included women). The idea of universal suffrage for free white men did not gain traction until the Jackson Era. Elections in this period were highly-restricted and delegative affairs - something like 6% of Americans voted in the first presidential election in 1788, and voting methods were all over the place, including methods like a voice vote (voting by paper was not universal, and secret ballots were practically unheard-of).
Wills is probably right to the extent that the 3/5ths Compromise gave additional House seats (and consequently more presidential Electors) to Southern slaveholding states* than they would have had if Congressional apportionment had been limited to the white population. Most of the Southern states had significantly large slave populations, and in some cases like South Carolina slaves were a large majority of the population.
*A note that in 1800 there wasn't as clear a sectional divide between a "free" North and a "slaveowning" South, as New York only adopted a gradual emancipation law in 1799, not freeing the last slaves until 1827, and New Jersey didn't adopt a similar law until 1804.
An interesting read is Jill Lepore's "How We Used To Vote" available through the New Yorker website.