Why do people think Michigan is a tossup but Wisconsin leans D? No way MI flips before WI! (Especially considering Flint)
Flint helps Trump. He is an outsider.
Higher African American turnout in Michigan due to a white Republican governor poisoning their families is not going to help Trump.
If Flint's problems continue to be painted as a Republican governance problem (I'm sure Hillary will also continue to work this angle), it will hurt his prospects in that state.
Virginia, there is no way you can connect Trump with a Republican governor or Republican governance. As I said, he is an outsider.
Clinton, on the other hand, is a Washington insider and part of the Establishment.
It doesn't really matter. People also blame the president for numerous things that aren't their fault, and take it out on the party in general. That is why it is so hard for the party that controls the White House to make any notable gains whatsoever during their midterms. Likewise, many residents of Michigan aren't going to be as receptive to Republicans while this water crisis still unloads fallout on them. Republicans have controlled the Michigan state government for decades, save for 2007-2011 when they only controlled the State Senate/AG/SoS. The whole issue is a clear picture of the failure of Republican governing principles in Michigan, and if you think most people are going to fully separate that from national party members, well, heh, that's wishful thinking.
Further, as with many other similar community disasters, turnout among Flint residents, and thus African Americans, will likely surge. Trump isn't going to be winning over African Americans, so the increased turnout will benefit Hillary. They like Hillary and clearly do not like Trump, at least according to favorability polls.
Finally, you're putting far too much faith in this outsider angle. The people want someone they can trust to handle the problem, and many feel like career politicians can't deliver on their promises. This would benefit Trump more if he wasn't such a lying, dimwitted asshole. Hillary is no saint by any measure, but if you think Trump is more trustworthy, especially given recent events, then you really need to have your head checked.