With the clutch depressed and the trans in gear, you're eliminating the trans, driveshaft, rear-end and wheels. Rev it up and if it isn't smooth, you have to look at your balancer, crank-rod-piston, flywheel combo. Has your engine been rebuilt by someone else besides you? Tell us whatyou know about your engine.
If it only vibrates at high speeds on the highway, you have to start at the wheels then move to the driveshaft. jack it up and rev it in gear.