I think it'll be close, but I still suspect Clinton will edge the main election. Trump's still in his post-nomination boost, where the party's rallying around him etc, and he's still got a small national deficit to Clinton. Enough states are toss-ups that he could win on current polling if the election were held tomorrow, but if most Sanders backers eventually fall behind Clinton then she should be able to cobble together a weaker version of Obama's 2012 victory (I can imagine Trump taking Ohio but Clinton holding Pennsylvania, Virginia, and Florida, which would be enough of the swing states to seal victory). If Clinton is hit by prosecutors, after the convention, and still tries to cling onto the Dem nomination, then Trump has a very good shout of winning. But that's a pretty unlikely turn of events; if Trump wins it will probably be a close race, mainly won due to Clinton completely failing to get out big chunks of the Democratic base (some level of reconciliation with Sanders is vital if she wants to produce a decent lead over the Donald). That's very plausible, but instinctively I suspect she'll just about manage to rope the voting coalition back together.
It's worth noting that Trump is now increasingly trying to turn to the GOP for funding, GOTV ops, and ground support, areas in which they lagged badly behind the Dems in 2008 and 2012. Trump doesn't seem to be doing much by way of putting his own operation together yet that will patch up the GOP's continued weakness in these areas, and in a close election that could really cost him.
As for the Libertarian duo, I doubt they'll have much impact not least because the only thing the Dems and GOP seem to be able to consistently work together on is shutting out smaller parties, which they do with absurd effectiveness (aka "you need to be getting 15% in the polls to get in the debates, Gary, and by the way the pollsters are mostly skewed to one of us or the other and won't actually include you in polling"). That said, they're getting a lot of media hype this year and with two very unpopular candidates they could do better than one might expect. Hard to know who that'd hurt more, honestly - on the one hand they might provide a home for disaffected conservatives; on the other, they could well scoop up some of the republican crossover votes that Hillary needs and some of the Sanders voters who want to kick the establishment without voting for Trump. I imagine they won't have much traction with a lot of Trump's socially conservative and economically protectionist supporters, so they might actually harm Clinton more if they do well.
