I edited and ended up losing the post and 'tis too late to re-write it all. Find out what the flies and larvae are and what they carry before you dump the stuff - it might be OK, but there is always a risk with viruses etc. But you do have too many fish and you gotta read up a wee bit on cycling and water testing. It really is important to know the ammonia - nitrite - nitrate process.
You've done a massive water change anyway, so the cycle is disrupted. Personally, I'd dump the filter stuff, clean it all out and start again - mainly due to the fact that you will have a new stressful cycle and whatever infection on top of that anyway, so it's a no-win situation. You'll have to identify your flies and larvae in order to learn what diseases they may carry - I've never heard of such a thing happening in a filter - poor you.
You do have too many fish for the tank - soz. Around 4-5 fish would be the limit. You seem to have more than one infection going on, so reducing the chance of deaths would be my first priority and I would be cleaning out the tank and filters and maybe carefully starting again in a bigger tank or at least using a bigger external filter with smaller, more frequent changes right now, making sure I placed my fish under minimal stress whilst the tank went through its cycle.
Small and frequent water changes lessen cycle disruption. Maybe your weekly 50% changes are causing continual flares and stress on your fish? Do you monitor your ammonia, nitrite and nitrate levels before and after you change the water? You may need to allow for your nitrates to build up in order to balance the water?
Forgot about the gill flap... You may find your fish will grow an extra bit back over his gill to make up for the problem - but only if water quality doesn't continue to be a problem. Keep him in nice, cycled water and he may be ok. But with gill and eye problems, he may now lose his balance. If he flips or sinks, he can live for years, so still look after him if he shows signs of this.
If you're unsure about how to read the test results, please get back to the site. The best kits are liquid drop tests - they are the most accurate. I'm fairly sure your kit will show high nitrates on top of other water problems. You may need to gently squeeze out your filter too.
Go and have a look in a big petstore and steal their ideas. Speak to the junior in there - they are often really enthusiastic and full of DIY ideas and don't try to flog you stuff. I go into Aquatic Design on Gt Portland St and look at their ideas and then think about what I can use that's the same. Hosing from B&Q has come in handy, as have bits and bobs from Muji. I've even sawn down pens to make spraybars for smaller filters. Greenhouse polypropylene shields harsh tank lighting and Xmas decoration suckers and many hair fastenings work marvellously well in tanks... Lateral thinking... I've even drilled a Paperchase acrylic pencil case into a drip filter to boost an undergravel filter in an aquarium. Cost pennies in comparison to a new unit.
You gotta get your water test kits - they're a wee bit expensive and time consuming, but they will give you answers. I think you'll find you have poor water quality, but you gotta act quite fast to prevent things flaring up for them in the future.
Do a 33% change today and same tomorrow and see how it goes. If the eyes are still cloudy, you may have to do bigger changes to reduce baterial numbers if the clouding gets worse, or smaller ones more than once a day to alleviate the symptoms. Is there fin rot that goes with it and does the fish look and feel a little bit fuzzier and redder? If so, I bet you've had a water cycle flare and you need to dilute the bacterial numbers that have arisen. Have a wee look at the spines of your fish though. Are they straight, or a little bit kinked? Do you have any photos? Are there any other signs of behavioural differences like clamped fins and resting along with the cloudy eye, or are the fish quite lively and taking part in the tank activities. How old are they? Soz for all the questions.
When my fish bred, I found what a real mix they were. They looked like veiltails and indeed most were slower fat bodied fish - but some still had some comet tendencies which were in their blood. My fish were real mongrels - your fish may be too. Some of my fat bodied fish could give some slimmer fish a run for their money. It really is dependent on the genes of your fish. Maybe a more pointed nose and some fin imperfection will alert you to the fact they are partial comets for example. In which case, they may enjoy some competition. I have one huge fish which is definitely a comet throwback - as was one of his parents. He is like a dolphin and just outstrips everything in the tank and could do with a faster friend I think. Even though he is an almighty coward and his smaller, fatter brother is his minder!
Shreds has floated to the surface as I worried he would, but he has once again regained his bounce and is flinging himself about big style. He is soooo loving the fact that he ain't a bottom-dweller anymore!