Opinions please on an input shaft.

[Dynogt17]

After having a man here help me line my truck back out after the mistake of a bad tune. The clutch was ruined(by the bad tune). Buddy that did the first clutch was to busy. Went to the stealership( i needed it fixed while son had a plate put in his head). They removed the clutch tuesday, installed new one Wednesday, removed it again Wednesday( kid left clutch disc out, Thursday back together, Thursday night kid cracked my pto pump. Got it back last Saturday... My issue is they said i needed a input shaft and bearing. I was charged for it. I now have a vibration about 50 to 58mph. I looked up in the inspection cover. From what i see the input shaft isnt new rusty & pitted. I have pics. Can you all tell me if im wrong thinking the input shaft wasnt changed?