The following circuits are lacking their ore dictionary entries in _oreDict.zs causing AE2 crafts to incorrectly assume they don't have the needed ingredients.

crystal processor -> circuitMaster
wetware processor -> circuitUltimate
wetware circuit -> circuitMaster
quantum circuit -> circuitExtreme
nanoprocessor -> circuitExtreme
nanocircuit -> circuitAdvanced
microprocessor -> circuitAdvanced
electronic circuit -> circuitBasic
primitive circuit -> circuitBasic

I've got a PR incoming if it's something we want to fix.

Also noted Wetware Processor Array -> circuitSuperconductor

I'm missing something. I made these changes on both the client and server and the circuits are still not working properly in AE2 and not showing ore dictionary entries.

All of the circuits are already in the ore dictionary.

What you might be missing is that AE does not craft anything except the exact items listed in a pattern, even with substitutions enabled. All that substitutions does is allow existing alternate items to be used instead.

Oh, ok, so related to this AppliedEnergistics/Applied-Energistics-2#2348

I've had a bad understanding of how that substitution button worked this whole time.