The work around I have figured, in regards to mining Infused Stone with the Digital Miner, involves using the custom XML file for the SAG Mill from Ender IO.
Make a custom addition to your SAG Mill XML file, requiring 9 of a specific shard type to create 1 ore block of the equivalent type. You can add these to the XML file using straight item id#'s, bypassing oredict requirements all together. This means that you would only need to collect 9 shards of every type, then you could have a block of each shard type and use it for your Digital Miner filters. It also means you could use the blocks for decor if you wanted to.