No no no
GPIO system module, DSP system module, those existed in 9.2; all N3DSes shipped with the 8.0 version of GPIO and DSP, so they were never part of the actual system update responses until 9.5 and 9.7 respectively, when they were updated to a more recent version. Meaning, most people who downgraded a N3DS, are missing those two components, which are mismatched and still on a higher version than intended. This can cause problems.
@drnkbeer You need to get those two CIAs from an O3DS 9.2 update pack.
I don't know the specifics, but GPIO handles input-output and DSP is for audio. I don't think the 3DS could even function without GPIO system module, and you would have no sound if you didn't have DSP system module (if the 3DS even booted without it.)
The amiibo one is fine, because that really didn't exist until 9.3; either delete it with FBI or leave it, as it won't cause problems.