For the 1.7.10 version.

When customizing the recipes, a itemName with a period is not read correctly. This will lead to a the game hanging on FML stage 5.

For example items.Railcraft:part.rebar

Here is the log output.
http://pastebin.com/p2dBwfr9

Also there is no way to specify an damage value.

I'd suggest removing the recipes customization feature and supporting MineTweaker3.

On that topic of MineTweaker3. When recipes.removeShaped is used to remove a backpack's recipe. I then can not apply upgrades. I suspect this is MineTweaker3 fault.

Supporting minetweaker, the config recipes are long gone at this point.