Yes, of course Trump will pardon Flynn and Manafort. I've been saying that from the start with Flynn, who has always been a Trump loyalist. Manafort has never had as clear path to a pardon, not being part of Trump's inner-circle, but if Trump thinks that a) Manafort hasn't flipped yet, and b) a pardon will prevent it, he'll do it.
What about state-level charges? A few brief comments. First, Trump will have to leave that to state-level Republicans to corrupt the legal processes at the state level. Second, even if state-level charges got either to flip, remember that it won't matter. Mueller doesn't matter. Mueller won't/can't indict Trump, and nothing that comes from the investigation could ever convince congressional Republicans to turn on Trump. They are the only ones who matter, and you'll pry Trump's ass from their cold, dead lips.
So, really, none of this matters. Trump suggested pardoning Flynn and Manafort as he has begun to enjoy his pardon powers, because of course he'll pardon them (Flynn, at least). But, it wouldn't matter if he didn't. It wouldn't matter if they flipped. It wouldn't matter if there were video. None of this matters.
Trump has already gotten away with everything.
Oh, and remember that unless the economy turns south, he'll be reelected too.