1. He shouldn't be reaching across the table to make change, nor making change at all mid-action. It's always better to let this wait until everyone's bet/ante/whatever is complete, to avoid any confusion. He should just post the oversized chip and wait for the dealer to kick his change back. That said, this part is a mere annoyance, not a major issue.
2. Even if there's a reasonable case for him to manage the pot (e.g., long table and he's sitting in the middle, a situation I'm often in), he should not be shuffling it or otherwise handling it longer than necessary. It's frankly a game-security issue. Bad enough to have done this at all, but then you ask him to stop and he keeps going. Still out of line, but maybe he thought it was okay because you just wanted a count, and he gave that. But then you ask him to stop again, and he keeps going, and you have to basically yell at him to get him to stop.
This dude needs to understand that it's not about you getting a count. He should not be playing with the chips that don't belong to him and are being contested by other players. Period, at all, ever.