Just spit-balling here, throwing it out there;
A misalignment in the bell-housing, YES it could cause a vibration...
a bit more info would help US help you some too...
A crack in the bell-housing isn't good,
replace or repair it...
Make sure to replace the missing alignment dowel pin too
{I assume, you were talking about alignment dowel pin, not a dial pin}
What engine is it behind ?
Is this a BB or SB what year & displacement ?
would also help
Is it on a steal crank engine ?
or a cast crank engine ?
they take different clutches, usually...
did you replace the pilot bearing/bushing when doing a new clutch ?
or check it for wear/clearances at-least ?
that could be a vibration problem too...
did you install the right clutch & have it centered properly,
before you tightened it down, using a proper clutch alignment tool
&/or do you have the correct matching flywheel/clutch combo
for either of the style of crankshafts mentioned above ?
the clutch could be out of balance, maybe threw a balance weight
the flywheel could be for an external balance engine or visa versa too,
{albeit that'd wrong clutch & flywheel combo, usually would vibrate violently}
or wasn't either wasn't balanced properly to begin with...
among other things like pinion angles or misalignment
or worn out mismatched parts etc.
good luck