I believe the EFI systems can deliver more horsepower, as long as you have proper flow-rate injectors and a sufficient fuel pump to keep them at full working pressure. I've used desktop dyno before, too - it is remarkably accurate. Honestly, carburetors can be a real hassle to keep tuned. EFI is so much superior for real-world driving, however, drag cars can forego the smooth-running attributes of EFI and just use a big honkin' carb (carbs do the WOT thing really well).
What year car do you have? As long as it is a 5.0 or 5.8 Windsor V-8, you do have the option of going "retro". :-)
My '65 Fastback is currently running an '87 5.0 engine, fitted with the old 289 intake manifold and distributor while the 289 is being rebuilt and balanced. *** Note: you've gotta run a Ford Racing Parts/SVO billet steel distributor gear; the roller-cam engines have steel camshafts that will chew up older engines' cast iron distributor gear.*** There are a few other early/late parts interchange issues, but it can be done.