Including support for mods that even tweaks recipes like MineTweaker. How would I retrieve a recipe that is also been modified by MineTweaker/CraftTweaker?

After the mods are loaded you can get a list of all the recipes from the various registries and then loop through them to see if you find a recipe whose output matches what you're looking for.

13 minutes ago, jabelar said:

After the mods are loaded you can get a list of all the recipes from the various registries and then loop through them to see if you find a recipe whose output matches what you're looking for.

Is it okay to do the lookup after the whole initialization phase. For example on events such as when player interacts with a block, it will loop through all the recipes to see the matching output?

Yes. If you think about it, the crafting GUI has to loop through all the recipes whenever you change the inputs.

For performance reasons you need to be weary of when you do this as there are thousands, perhaps hundreds of thousands of recipes. So searching it takes some time. So do it as rarely as you can, and cache the results.