You could still use AE autocrafting.
- Set up a chest.
- Give your AE system all the patterns it needs for your final craft - if you're making 5x cobble, give it the recipes for 1 through 5.
- Connect a precise export bus to the chest.
- Tell it to export 5x coompressed cobble into the chest and then set the mode to Craft Only.
- Connect an import bus or a storage bus to the chest to make the final materials available in your AE network.
You might be able to substitute the chest by connecting the export bus directly to an interface, but I'm not entirely sure if that would work. I'll have to test it.