Hmm... while that setup
could be prone to excessive vibration, given it's an almost straight shot down I'd imagine that'd not be an issue, but I'd still consider rerouting, strapping it to the frame w/stand offs if possible, tho on yer bike that could be tricky... I also forgot to mention it was the carb shaking too that made the prob so bad for me.
A few black specks aren't going to effect the filter, tho it's good you flipped it around

If in doubt, jus pull the carb end and drain into a bucket/gas can for at least 30sec to a full min, this will show if yer not flowing/venting properly.
Black isa lil dark for these motors, even during break-in, I'd shoot for a milk chocolate brown, cooking chocolate if yer paranoid
edit: Oh and BTW that's a sweet build ya got there!