Unfortunately, I can't help you there...I never really found them either.
I DO know that you can get a TON of the one-yen pieces from those black tadpole noise, but I still son't know where to get Shadow Matter...someone told me at one point that the only way to get it is to beat a certain boss on either Hard or Impossible, but I don't remember which one...
Naw, I beat him after a couple of Cordyceps, and leveling up some pins. I've finished all reports but Another Day at this point. I am, however in need of Visionary Blend, and I can't find a good spot for getting the low-yen pins... and Dark/Shadow Matters. Have you got any helpful hints?