Theoretically you still have some issues, recipe changing has been done before, many times. Unfortunately its not quite the simple that still leaves a lot areas broken. These include weaponry, mobs, hunger, crops, metals, world gen(that's the big one). TFC has its own world gen system, and its own health and damage system, fixing these have been attempted before and there certainly have been partial successes (Railcraft, Buildcraft, and Thaumcraft minus a couple pieces at seperate times were the main ones) I have yet to see anyone even generate their own ore in a TFC environment.
I'm not saying it can't be done, I'm just saying its not as easy as just using custom stuff.