The clutch can be pressed whenever as it really just pops it into neutral. When you're going slow, like in traffic, you can keep the clutch down if you feel the rpm is going to low like the car will stall. Thats fine.
As for the OP, when you're shifting at high rpms, I've never had the vibration feel so perhaps you're keeping the clutch depressed too long? If i shift at high rpms, I'm in and out of the clutch pretty quickly.