Why did my 2001 4.6 liter Mustang GT V8 make "only" 260 HP while today's base Dodge 3.6 liter V6 churns out almost 300 HP? Both benefit from fuel injection and ECUs.

Your 2001 Mustang's 4.6L V8 uses old tech from the early 2000s: port fuel stuff, simple ECU set up, ...