Restoring a 1972 240Z, in the process of replacing the stock exhaust manifold with a new stock manifold. The old manifold has the smog tubes in the manifold extending about 4" into the exhaust port. The new manifold does not have the smog tubes, but the manifold has the ports for the smog rail to be screwed into the exhaust. Do I need to remove the tubes from the old manifold and install them on the new manifold, I will be installing the smog rail to keep the car looking original. Is there any performance issues with installing the smog rail without the 4" smog tubes.

Not that I am aware of, I went for a header w/o any smog gear on my 73, and she runs NICE. You would get better flow seeing how there is less exhaust to exhaust. (I THINK)

The purpose of the long air tubes was to direct fresh air against the hot exhaust valve in the hope that this would encourage more complete combustion. Removing them, and just pumping the air from the reactor pump straight into the manifold will not hurt your engine performance. In theory it might reduce the effectiveness of CO reduction produced by the air injection system. (If in fact that system actually accomplished anything measurable beyond simply diluting the exhaust with fresh air.)

The tubes themselves restrict exhaust flow and in theory should hurt performance, but only at high engine speeds.