IIRC the shop stated “engine still vibrates with tranny pulled back” (out I assume-jrrr)
Usually by 2500 rpm any signs of a missing cylinder ( or even two ) are gone. Lost in the 60 degree V. Smoothed away. For a vibration to appear at middle revs is unusual.
What could possibly create a vibration in a naturally balanced dual inline six at middle RPMs but not at idle? And OP already eliminated all belt driven systems.
Damper or torque converter are pretty much the only contenders I can think of.