That's great that you have a good fish store that you can rely on.I wish we all had one of those in our neighborhood.
Your tank is overstocked for sure.We try to recommend not owning a Koi in a fish tank to begin with,and that all Commons/Comets receive at least 15-20 gallons per fish to start with as they grow pretty big themselves and need plenty of space to swim. I would guess that changing out the water at 30% once a week would not be enough to keep your tank params ideal.
What you are describing on your fish sounds like a cyst/lump,which is sometimes common in goldfish.
The only thing is that if that lump appears all of a sudden out of nowhere,and it's tinged with red,it should be treated as bacterial.Once that swells and bursts,an ulcer will be present,and that in itself can be a problem as bacteria is able to invade even more.
It sounds like you've had fish for a while,but my advice to you would to be get your own Drop Test Kit,so that you know what exactly needs to be done with your water params.
Without knowing any exact number's,I would also advise to change out at least 50% or more on a weekly basis,along with very good gravel vacs.
I personally would start treating the fish with medicated food asap.If you don't have any,The Goldfish Connection has Medi-Gold that does an awesome job on sick fish,and food is the fastest way into a fish's system anyway.
Pristene water though is the first thing that you need to have though.
Does your water read an ammonia level right out of the tap,or have the ammonia levels always been high because your tank is so overstocked?ON an established tank,all ammonia/Nitrites should be reading 0---The best place for Nitrates is under 20 ppms,so that's where your tank really needs to be. Water born Meds are kind of pointless if your params are not in order.