You have achieved the function of auto-pattern making with JEI:
*Patterns can now be made with items currently showing on JEI. ( This is overriden by Just Enough Energistics. )
However, in most cases, i found simply filling slots with items that already exist(or patterns that can make the item exist) in the storage system would be more convenient for making patterns.(especially when there are a lot of item that can be used to craft a certain item)
I hope you can change it back, or add an option that can choose to fill the pattern with items in the ME system.