Yes.
Carbed fuel pumps are typically mechanical, and driven by an eccentric on the camshaft.
FI fuel pumps are electric, and develop higher pressures (WP for a carbed pump is 3-5psig, usually - FI WP is up around 45-50, and a regulator is involved.)
Also, the FI fuel pump is usually rated to deliver a higher volume. Since the volume of fuel delivered to the engine is controlled by injector pulse width, that's not a problem - but it should still be considered.
You can probably switch out the "stinger" assembly in the fuel tank and install an FI pump that way, then just run the wiring back. The fuel level sender should work the same, so it's just a matter of running power and ground back to drive the fuel pump. And, switch out the soft parts of the fuel line for higher-pressure fuel hose (due to the higher pressures involved.) You'll probably also need to reterminate the engine end of the thing, and provide a return line, since you don't have return lines for carburettors.
And, you'd have to bring the electronics across to make the fuel injection happen.
However, you should be able to either install the intake and carburettor on the later block (probable) or just swap the carburetted top end onto the FI short block (very likely) and swap it that way. You can replace the OEM carburetted fuel pump with an electric carburetted pump (spec'd for 3-6 psi) without too much trouble. Why for are you swapping the engine?