How to find a neutral to ground short on my main panel
AFCI's do have GFCI-like characteristics, because most of them include a &quot;mini-GFCI&quot; for detecting hot-ground and neutral-ground arc faults. That means you must handle their neutrals like a GFCI.  (certain GE breakers are an exception).  However, an AFCI will only trip due to neutral or ground mishandling downline of the AFCI.  You need not search for neutral/ground challenges on the panel side; even if you wrongly put the subpanel's neutral-ground bond back in, the AFCI wouldn't notice that.
It sounds like your subpanel's neutrals and grounds are wired correctly based on your description.
Neutral is not ground.  All grounds should be connected together.  Neutrals should only be connected when their partner hots (the ones in the same cable) are connected via wirenut, device, switch etc.  When 2 circuits are in the same box, their neutrals must be kept carefully separated.  &quot;Gray&quot; is an allowable color for neutral, so feel free to mark one circuit's neutrals with gray tape.
Next, you need to carefully review the instructions for the AFCI and assure you installed it correctly.  Seriously.
Next, it is a matter of &quot;divide and conquer&quot;.   You have left several appliances plugged in and haven't tried unplugging them.  You really ought to try that!   Now try removing circuit hot and neutral from the AFCI device - if the AFCI still trips, that tells you quite a lot. Then, re-add parts of the circuit one segment at a time until it trips - that tells you what part of the circuit it is in.
Steady on; ask questions.