Hi Newguy
Well do I need to say that overstocking is your major problem. Ok this is what you need to do. Right now changing your water is the only thing that has not killed everything. Tell me what kind of filter you have. Continue using rain water if you can, the high amounts of lime will drive your PH crazy. Also if you plan to do a bigger pond, Make sure you do not use any Lime rock in the pond.
Start out by testing your rain water PH, here in Pennsylvania it is usually around 6.5. If you are able, add a air bubble to your rain water harvest and attempt to keep debris out of the water. A simple air stone will cause some circulation. Do not get water from a lake, you will be bringing what ever parasite is in the lake into the pond.
Second, Never use any item that will make the Ph go down like an acid. Pick up a Kh test kit, Kh or Total Alkalinity is a buffer that prevents massive ph swings. In the day your plants are pumping out CO2 with photosynthesis. At night they stop and your Ph would crash if not for the buffers provided by Total Alkalinity. This is why when you add a ph down it only lasts for a few days. However, if you add enough of it, you will wipe out your buffer completely and crash your Ph. Ever hear of people waking up in the morning to find a pond full of dead fish. Or, when the ice completely thaws.
This is what to do....buy a large bag of Baking Soda. Yes, baking soda is a base, but Baking Soda is your best friend. Start doing 25% water changes every few days for a week. You need to restart your pond. Every day dissolve a fourth cup of baking soda in a gallon of water and pour it into the pond. Try not to get it directly on the fish. Baking soda will only take your Ph to a max of 8.6. Anything above that it will slowly lower your Ph. Plus Baking Soda is how you build up that precious buffer. 8.6 ph is fine for koi, a little high but its ok. After the week, dissolve the 1/4th cup after your water change. If you have heavy rains, add another 1/4th cup...it wont hurt them.
Think about either upgrading your filter or donating a koi or two. Another tip, if you have a waterfall, get a bag or crushed seashells from your pet store. Put them in a woman's stocking, rinse it really well, then place it somewhere where it will get good water flow. This will also stabilize your PH.

Good luck with your fish, hope this helps...Craig

I run a video blog on youtube, check out Craiggers Koi and Garden Ponds. I just enjoy talking about the hobby.

The filter I use is a TetraPond Pond Filtration box
http://www.petmountain.com/product/submersible-pond-filters/11442-517343/tetra-pond-tetra-pond-submersible-flat-box-filter.html?utm_source=googleproductads&utm_medium=cpc&gclid=CJa9h5vGlMACFQqGaQodZbMAQw

I understand it's kinda small but I do keep it clean.

The citric acid I used was this one: https://www.morgancountyseeds.com/store/index.php?_a=viewProd&productId=2334 from what I understand it buffer's and shouldn't crash right?

*It suggested 2 oz per 100 gallon I did maybe 1/3 out of fear of the PH dropping to much.

I'll try that crushed seashells idea not may pet stores around here I might have to order them.

/edit j found an old (10 years old) KH tester was 3drops started to turn 4 fully turned yellow so 3.5ish dKH (62ppm) from what I've googled I should aim for 2-3x that and baking soda should do the trick.

This post was edited by Newguy27 on Fri, Aug 15, 14 at 2:47

Update:

I did a water change, added the baking soda, and some crushed oysters shells on the waterfall (should work the same as sea shells?) and got a KH of 5-6 drops.

I understand that's still low but last night/today my PH went from a low of 7.2(nite) to a high of 9.0 (day) shouldn't it be a bit better? or do I need to give it more time?

/edit I think it's the water I'm using. It's old and in a underground cistern. I think the 56ppm TDS may have same lime messing with it.

Going try to catch some fresh rain and stock pile R/O it may take me a week but I should be able to do a 30-50% water change.

This post was edited by Newguy27 on Tue, Aug 19, 14 at 1:06

hello kraigger7, I'm new to forums altogether, please excuse any of my communication screw ups.do i understand correctly you use baking soda to help bring ph under control. I have an 800gal. pond with a bio filter and water fall. my confession of shame is that i intended to top off my established pond by adding 2-3" of city water and forgot it was running .3-4hrs later i freak out when all of my beautiful koi are dead. anyway the ph is about 8.o and i want to lower it. i could use some help and insight. thanks.

Use baking soda as an 'emergency fix'. You can't raise the pH too high, or lower it too low with it. Literally it's a miracle fix, but only for a short time. Once it's back to normal, introduce some buffer to the water through crushed oyster shell or similar. Your pH will no longer fluctuate. I've attached a very good article outlining the chemistry of ponding, and regulating pH.

http://www.colorbat.com/aquaclub/white/Meeting_July23/Aqua_Club/pond_running_on_empty.pdf