Hi Rapid, first let me say I'm sorry for your fish loss. I am a bit confused, you live in zone 5 and your lowest temperature was 40 degrees. I'm in zone 6 and had a very harsh winter.
Red Pest is a made up disease. I can read your mind, "then why are my fish dead". Red Pest is the ending signs of septicemia. Septicemia is of course blood poisoning. This can be caused by many things, the most evasive being an external parasite. You had mentioned you filled your pond from a local lake previously. This I wouldn't do again, any parasite in that lake is now in your pond.
Protecting our finned friends can be a major task. If you have a gravel bottom pond, that parasite may be living in the bacteria of the muck in the gravel. I would think about treating the entire pond in the spring if you haven't already.
Now, why do our fish seem to die off more in winter?During the warmer months, our fish's immune system is better prepared to defend against parasites. During the winter months, the fish's metabolism slows down. It may become stressed due to the cold, and their immune system becomes compromised. I believe it is below 40 degrees of water temperature that a koi will become more susceptible.
Heating a pond is a good idea, there are many systems to chose from. I'm currently trying to figure out a way to keep my koi pond heated. Koi just seem to explode in size when in a year round temperate pond.

I hope this helps, I would treat all your fish as infected for right now.

Craig

Thanks Craigger7, I guess the obvious question is, what do I treat the pond with and will it be affective at the current temperature which is about 43 degrees.

I agree, temperatures compared to out east are extremely mild, but yet I still get these bacterial diseases.

I total thought I was getting all these nasty bacteria from the lake, and I was extremely careful only to put in clean water between fall and now to make sure I didn't introduce any addition bacteria that they couldn't find off in spring. I had a biological filter which took care of any bad bacteria before the winter, so as far as I could tell, I had a pond with no bacteria.

I even turned off my other two ponds which feed this pond for the first time which collects lots of leaves. My main has very little muck and I made sure I cleaned out any leaves, I basically could see the bottom of the pond floor with a few, very little gravel here and there.

I didn't do any water changes between fall and spring as I didn't want to stress the fish out.

My questions really are

1. Should I be thinking about an indoor pond of some sort, do people do this at all ? I was thinking I could buy a 300 Gallon stock tank or something and get it prepared during the summer. I really don't want to, short of this, I think I will have to give up koi keeping and just stick to gold fish.

2. Do I do want changes during the winter and how many and when ? Will this improve water quality and reduce the bacteria ? Again taking portable water that we drink, so water is as clean as you can get it.

3. What medication will work during the winter on a large pond 1800 gallons and will it be effective ?

Are certain types of koi just more susceptible to deceases and a bad breed. My most recent one, I bought 3 from somebody, where very healthy and looked strong, but not strong enough to fight the bacteria.

Thanks

Hi Rapid
It does sound like you have a nasty bug. If your water is not freezing over winter, your really not putting too much stress on the koi.
To answer you question, yes people do have indoor koi ponds. These are usually those who are really addicted. I must confess I was thinking about it. If you water is not dipping below 40 I would not worry about it.
This is a tough one, but this is what I would do. It's safe to say, all your fish are carrying the protozoa. Septicemia in koi is highly contagious, it had nothing to do with the koi that you bought. I would look to purchase something that you can set up in your house as a sick tank. Either a small pre-mold pond or a large aquarium. You are going to have to treat all your fish and its best to do it in a small system, also less costly. Do a search on treating Septicemia in koi, I just did and there is tons on information.
You can do this now, just remember to slowly adapt the fish to the new temperature. Next, can you get water from another source other than the lake? I would drain the pond, clean it out of as much muck as you can. Then refill it and treat the entire pond. I don't see how medication wouldn't work at 40 degrees.
Again, I would not blame the koi you bought, you just have a bad bug. This happens from time to time with us. Now that you have the sick tank you can set it up as a quarantine tank for any new koi. Heating the pond would help later on, but that is your decision. I really wish you good luck, you will get through this. Goldfish....bah!!!

Craig

Thanks Craigger7. Appreciate the response.