2000 Saturn SL1 Bucking after clutch repair

After clutch repair, I find that I can engage the clutch smoothly going into first, fourth and fifth, but going smoothly into second or third is much more difficult.

I started noticing similar problems about 2 months before the clutch failed. At the time I thought it might be an ignition problem. Before the failure I did not associate the bucking and hesitation with specific gears. The association might have been there, or maybe not. When the clutch failed, I could feel something was wrong with the clutch pedal. This symptom developed very suddenly.

During clutch repair, the dealer also replaced the throw-out bearing and the electronic ignition module.

History. Car's quill bearing was replaced under warranty. About 33K miles, transmission bolts failed and transmission fluid leaked out. I immediately had the car towed. Repair record from that repair showed "clutch plate all torn up". After this repair I noticed a pulsation in the clutch pedal in the first inch of travel. When fully depressed, there would be no pulsation. The dealer refused to acknowlege this as a problem. So my question is this: Is it possible for the transmission to wear in such a way that the clutch would engage sooner in some gears than in others?