Would the south have won?
For much of 1864 Lincoln himself had doubts about being re-elected. It wasn't until the fall of Atlanta and John Fremont and General Cochrane dropping out of the election when Lincoln's re-election was assured. Assuming that either of those men stay in the running and the Union fails to capture Atlanta I can see McClellan winning.
What happens after that, however, depends on whose direction the nation follows: the pro peace Copperhead Democrats or the pro war Democrats and Republicans. If the pro peace Democrats control either house of Congress it is possible that the South would "win" (I say that very loosely as I doubt the ending of the war would be very favorable for them even if they retained sovereignty). However, if McClellan has the support of a pro war House and Senate I think he would've continued pursuing the war like Lincoln did. It would take a little longer due to his cautious nature, but inevitably the Union would've won the war.
I also think that McClellan (in the event that Republicans don't gain a super majority in Congress) would've been very lenient on the South in the aftermath (maybe some Reconstruction but I don't see any serious movement to push forward any Civil Rights Act or *gasp* end slavery for good).
