all engines vibrate to some extent while running,
if your only feeling the vibration in the shifter, thats obviously not excessive,
if the shifter or linkage is touching or intermittently bouncing off a minor contact point in the trans tunnel,
or the shifter is loosely mounted, the noise generated will be a huge annoying P.I.T.A. without any doubt.
yes any water in a glass seated on most engines will show vibration
,especially if the cams designed to provide a bit more upper rpm power than stock
as youll have at least some minor LOPE or SURGE in the idle