Manual transmission, from second gear through fifth, I have a vibration as the rpm's climb, and it is making a scraping sound when it is moving

Recently my clutch hydraulic line developed a hole and completely drained while sitting cold. I changed the line and master cylinder at the same time, i have bled the system and i gave plenty of clutch pressure. The gears switch out with ease, but from second gear through fifth, I have a vibration as the rpm's climb, and it is making a scraping sound when it is moving. I should ad that it has a new clutch with less than 10,000 miles on it. I know that it is not my engine making the vibration, and there appear to be no leaks. Can you tell me what is causing the vibration? it seems as though it is slipping some when this happens. There were no problems until the fluid drained the initial time, and I changed the line.