Setting Up A River Tank - Littlefish

It's been a busy day.
Rather than move the fish to the 200L tanks, I moved the wood that was soaking in the 4ft Aqua Oak tank in the spare bedroom, cleaned the tank & used that.
I've have spent many hours rinsing new sand & rocks from my stash of tank stuff, and draining the river tank to a point that I could actually try to catch fish. I didn't want to disturb the substrate any more than necessary, but I had to remove the plants.
The following have been transferred to the other tank:-
3 bull dog plecs
7 panda garras
8 rainbow shiners
9 hillsteam loaches
8 gobies
6 amano shrimp
2 assassin snails

I knew I'd lost a lot of rainbow shiners, and now only have 8 from the original 24.
As for the gobies, originally I had 10 cobalt blue and 8 annieae. At this point the 8 that have been transferred to the other tank are so pale that they are difficult to identify.
I still have all of my bull dog plecs and panda garras, and have lost only 1 hillstream loach.
There is still some movement in the main tank (I've already had to stop typing once to catch more fish), and I've always been particularly rubbish at finding/catching shrimp, so I'm stopping for a break before I remove more water from the tank and have another go at locating any remaining signs of life in the tank.

You're doing everything that you possibly can in what is such a sad situation.

In an effort to help get to the root cause, aside from some sort of chemical pollution, is there any possibility that the FX6 might have been too strong and potentially a cause or contributor? A couple of years ago, when I transferred my 3 remaining ailing pygmy cories into the QT, their demise was dramatic/sudden and swift albeit they were weak to begin with; it struck me too late that the filter I was using in the QT was far too strong, even on its gentlest setting, and they were getting buffeted around and thereby unable to rectify their swimming position while one sought refuge on the filter bracket - I tried switching the filter off for a while but by then it was too late. At the time, I did find an article which indicated that fish could 'drown' albeit rarely / gas bubble disease could form. Others (esp Sue) may know more and have a view on this? It might be worth getting her/others' views on this, just to be certain whether resuming the FX6's use in due course would be fine or potentially best avoided.

I really hope the situation settles and the remaining inhabitants show signs of improvement in their new tank.

@Littlefish my first thought would be that this is unlikely, unless you chose completely unsuited fish (and I completely don't believe that) the flowsrates that are possible in a tank will never reach river flows. At best rou might be able to achieve these only as the water leaves the manifold and the average will be relatly small with areas of little flow mid tank somewhere in the water column. If that were the problem I'm sure the fish would find them and settle there. You could look at the flow rates using an airline attached to a stick and watch for the bubble flow pattern across the tank in various places down the tank to put your mind at rest?

No dead fish in the new tank this morning. The rainbow shiners are quite active, but most other fish are still hiding. I think that this is possibly due to the lack of shiners mid-water, and I'm hoping that getting some plants for the surface/bunches of elodea attached to suckers on the sides of the tank will create more cover and encourage the fish out of hiding, if only for long enough for them to eat.

I've put some plants into the temporary tank and some of the fish have started to explore.
I plan to completely strip down the river tank, clean everything (including the hoses & pipes), and set it up again. I'll probably make some minor alterations to make things easier to clean as well.

I've lost another annieae goby overnight, but the rest of the fish seem ok, and the water parameters are fine.
I've been to the local MA to see if they had any further ideas on what could have gone wrong. They said the same as has been discussed here, and the manager talked me through their systems to give me some ideas on how to change the river manifold to include an extra hose & tap to be able to flush the system to waste and ensure that it is cleaned on a regular basis.
Stripping down the tank, making the changes to the manifold, and setting the tank up again is going to take a while. It's quite a complex system and althought I took a long time researching the set up originally, considering I've only been keeping fish for around 2 years, I still think I may have over-stretched myself with that particular tank. I'm kicking myself that the fish have suffered for my lack of experience, and am determined to ensure that the new set up provides the fish with a better environment.

That must be such a relief for you  It is so hard to watch fish die and feel helpless to do anything to stop it.

Great to read this better news. 

The fish are still in their temporary tank. I've tested the water and the results are 0, 0, <40, same as always, but they don't seem to be feeding as well as they used to. Perhaps they still need more plants & cover to make up for the depleted number of mid-water swimmers, even though they have a lot more cover in this tank that the other one.
It's been a week since I had to relocate them, and although I've had no further deaths, the fish just don't seem to be themselves. I'm a little concerned. The temperature is 19C, there is plenty of oxygen (4 port air pump & airstones), and the original fx4 is running with the new hoses from the fx6 box. Most of the fish are out and resting on stones or attached to the glass, and the remaining rainbow shiners have some lovely blue colouring at the moment, but the algae eaters mainly ignored their courgette on Tuesday evening, and have been the same with Repashy coated wood & rocks yesterday and today. They used to go nuts for the Repashy food, but not now. 

Agree that the shiners will benefit from more numbers and the other fish will appreciate them too.  Not sure if the other fish need company as such?

Mosy likely you will want to have the main tank set up again first though... maybe a slow reintroduction of fish species by species may be required to be on the safe side?

I'm struggling to offer any more advice or thoughts im afraid...