Firstly, I've been keeping fish for around 10 years and have kept a wide variety of fresh water fish, with about the only exception being discus, they've just never really interested me! I currently have an 80g (120x50x50) and a 45g (90x45x45) and I'm in the process of setting up a 160g (150x70x60). The big tank was supposed to be home to my large datnoid and ornate bichir, and possibly an asian arowana if my bank balance allowed. I've always had a soft spot for clown loaches, and have kept several groups for many years. I currently have 9 around 10-16cm in the 80g and 4 4-6cm in the 45g. I'd always thought about doing a large tank with a big group of loaches, and after reading Emma's article in the May PFK magazine, and talking to my girlfriend (who loves the loaches and isn't so keen on the big dats or expensive arowanas) we've decided to set the 160g up as a loach tank with my current 13 and probably ~20 small ones from the LFS. They'll be living with a selection of south and central american cichlids (heckelii, surinamensis, balzani, sajica and uaru) that are growing out in the 45g and another small tank. I'll post some pictures when I get it all set up...
Anyway, my question/problem. The 80g had some dark red sand as the substrate (an experiment to try to get better colour out of the dat and ornate) which I had gotten tired of. The tank is pretty crowded, but well filtered with a big wet/dry sump and a canister with a UV steriliser, and the sand was hard to siphon and keep clean. So, while doing a large water change last Saturday I siphoned out all the sand, and replaced it with a thin layer of well washed gravel I had from another tank. Tonight I noticed the loaches weren't looking very happy, and a couple looked like they were getting cloudy eyes (one was quite bad and another two were showing signs). I did a quick search and found it could be from bad water, so I tested it. Shit. Nitrate ~20, nitrite ~ 0.25, amonia ~3.0. I've changed the substrate several times in the past year with no problems so I'm not sure what upset it this time. I've done a 40% water change tonight, and I'll do another tomorrow morning.
What I want to know is will the cloudy eyes heal/improve with good water or is the damage likely to be permanent? I've added some salt, the temp is around 26-27C and the pH is around 6.0.
Is there anything else I can do to help with the cloudy eyes, malafix or other meds? I feel so bad that such a stupid mistake as not keeping an eye on the water after changing the substrate could have permanently damaged my loaches.

Cheers,
David