J, my body had the same reaction went off cheese burgers!
There are a couple of possibilities here:
1) the gas released from the decay in the disrupted stone bed effected your fish.
2) when you removed the rocks and plants you removed the bulk of your filter bacteria. Upgrading a filter system is mandatory when you remove the rocks. In some cases, depending on fish load, the biofilter will catch up to the ammonia output of the fish in a matter of a few weeks. Don't feed during this time. DO do ammonia tests and nitrite tests and let us know the readings.
3) the stress associated with the removal of the stones and/or increase in ammonia due to the removal of so much 'good bacteria' along with the bad, has set up an opportunistic parasitic population explosion. If you have a koi club in the area, contact them and ask who the KHA ( koi health advisor) is and if they would come over and 'scrape' your fish for parasite identification and recommended treatment.
Unfortunately this is not a good time of year to be working on fish ( depending where you live of course).
JR