4 spd...Dulp!
Push'n clutch in should determine trans.

A wiped lobe or collased lifter will make it run ruff. Wide vacuum readings.
Can still do the cylinder check pull'n 1 wire at a time.
If me, i'd pull and tear down(assemble my own). Take no chance of major damage.
If shop assembled, let them do it.
If they built and assembled, you didnt mess with internals, everything fine on break in, i say thier fault.