Usually, with the foot resting on a vibrating clutch pedal, its an indication of diaphram fingers not the same height from the flywheel.
But, with a new clutch, it might be an unbalanced flywheel. A chip may have gotten between the flywheel and machine's bed and planed off some material. Now, the flywheel would be thin on one place, and thick 180 degrees on the other side. Kind of a long shot, but, possible.
One can remove the input shaft from the trans real easy. Place the trans upright between two tables with the input shaft pointing down. Place a drain pan underneath the shaft. Remove the bearing retainer, and pull off. Might want to replace the bearing retainer, pretty cheap. Pull on the input shaft carefully straight down. There will be some needle bearings come with it and the fourth gear synchronizing ring.
For re-assembly, apply grease to the inside of input shaft, insert needle bearings into grease, place greased synchro ring onto shaft. Carefully insert shaft into trans making sure the three pawls engage with the three slots on the synchro ring. Tighten bolts when bearing retainer is mated to surface. Fill with oil after installing into car.
Everett "OBJECTS IN THE MIRROR DISAPPEAR UPON RAPID ACCELERATION"