I presume if the shifter poked him in the leg it is a manual. If the shifter was not changed, I would first check the linkage, perhaps a bushing came out of a piece of linkage which contributed to sloppy shifting.
Other things to check. I am not a Chevy guy, but would presume they use slave cylinders and diaphragm clutches. Perhaps there is air in the hydraulic lines.
Was a new clutch installed, and was the flywheel resurfaced, that could provide chatter. Also was the throwout bearing changed.
Was the clutch plate properly torqued to the flywheel? I had a loose bolt on a flexplate give me trouble once.
A shaking truck is not a function of a manual transmission unless its mount is shot, and that only shows at higher speeds.