I remember seeing something on the forums a while back about some sort of 'perfect' config file etc for WinUAE. ummm.... can't remember what it was called...
I think the so called perfect config for Winuae you saw was for running old games, I seriously doubt a Perfect config even exists,
i found WinUAE what came with AF4 was really slow but WInUAE what came with AF5 is really great and i still use it as the latest versions seems to be getting worse after each update,
for speed and a reliable version i would say get the Winuae version what came with AF5.