That sounds like the first mod ever made for Freedom Force called "Avengers mod" It had the same Campaign but like you said, it replaced the in game characters with Marvel ones, but they all didn't equal their FF counterpart (Mentor was replaced with Hawkeye). The head nifs were changed to the Marvel characters but the voices stayed the same so Hawkeye had Mentor's lines and voice which didnt flow very well. Also I remember Thor used the Order mesh with a Thor skin on it, very old school!
I actually have that mod on my hard drive but I don't know how I would get it to you unless anybody else has a idea.