So sorry to hear about all your fish losses!
Fish don't do well with quick changes. I suspect it was just too much for them all at once.
There are quite a few possibilities and no way to know 100% sure which were the actual COD, but going forward, if you ever face anything like this again, here are a few things I'd do differently:
When you go to replace substrate, drain most of the water out of the tank but leave a few inches in the bottom. Then do a really deep gravel vacuuming- sucking as much mulm (brown gunk) out of the substrate as possible. KEEP IT and lay this back down in the tank right before adding the new substrate. This mulm is FULL of N-bacteria and can really help the new substrate cycle quickly. A LARGE portion of any cycled tank's N-bacteria population is actually found in the substrate, as that has the highest surface area of any other portion of the tank- including the filter.
Any time you're making massive changes in a tank, keep as much old water as possible. This will help minimize all the chemistry changes (many of which we don't have hobby-grade tools to even measure) that the fish experience going into the new environment.
Be really careful with Prime dosing. Do NOT overdo dosing, as the way Prime works also strips O2 from the water, and this can be a problem- especially for larger, oxygen-demanding fish like cichlids.
Eco Complete has experienced several quality control issues over the years and people have ended up with batches where the liquid has gone toxic. I don't know if that is what actually happened in this particular case, I haven't heard of any issues recently, but it is a possibility.
At this point- I'd probably do at least one or two large water changes on the 90gal (at least 75% each time) just to try and make sure there's nothing funky going on with the water chemistry, and then start over. A single pleco in a 90gal tank shouldn't produce enough ammonia to even register on a test kit, so I'd probably go ahead and move him back in there and plant the tank. Then just stock really slowly from here on out, maybe a few fish every week, to slowly build up your N-bacteria colony. As long as the tank is well planted and the plants are growing, and you don't stock too quickly, you shouldn't experience any ammonia spikes.