A few comments:
Neo-Confederates and Neo-Conservatives are not necessarily the same. (Lott's the former, McCain's allies are the latter.) Try and disambiguate them.
If McCain was nominated, it would be far likely that Florida would be a lot less close. He was far more popular than Gore in 2000. (Though the African-American vote would be almost all for Gore, with Lott on the ballot.) Plus, Harris would be a lot less enthusiastic to campaign for McCain, since she was such a Bush supporter. (And, given McCain's calls for an investigation of the SC Poll Closings, he'd shy away from things like the "felon list*".) You'd still have the butterfly ballot, though.
First off, Rove may not have been willing to work with Lott without a major backlash from McCain. He was mad as you-know-what over what Rove did to him in SC. And, there were enough damaging things about Gore to sink him IRL (Occidental, Campaign Finance) even with a weak candidate like Bush**!
With Hunter as SecDef, and Cheney out, you may have nearly butterflied away Iraq.Of course, since McCain did make no bones about his "Rogue State Rollback" plan...
* Said list is in quotes due to it containing people classified as felons who A. Were only convicted of misdemeanors B. Were of a different race or age C. Were convicted in the "future" (I.E. after 2000)
** Of course the media didn't ask about Bush's questionable NG service, his possible perjury in the Eliza May case, his possible drug use, and the poll closings in SC.