As an update of sorts, I have been slowly working toward getting everything cleaned up. Yesterday I poured peroxide over everything and let it sit for 10-20 minutes then I hosed it off and began scrubbing each piece with a firm toothbrush till I thought I got everything off, then soaked them in water, Today, I noticed that there was still some of the brown mold webbed across many pieces still, so I got more peroxide set the affected pieces in a bucket then poured it on. I plan to let that sit much longer than before, maybe overnight if possible. The brown mold has proven to be very resilient thus far so the battle still continues.
On another note, while I was doing all this I came across an co-op sponge filter that was sitting in a tote that had substrate with standing water in it and it looks like it could have white patches on the sponge and most likely the air stone in it as well, would I use peroxide on this as well or would just soaking it in clean tap water be sufficient to clean it?