The coupe we put the L series in had a manual tunnel. I had to remove the original gearbox mounts and radius the gearstick hole slightly for it to fit with the stanza box. There was a small amount of persuasion required at the front of the tunnel needed for clearance.
It was running twin dellorto's. There wasn't an issue with bonnet clearance.
I'll see if I can dig out some photo's.